Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T34234 Target Info
Target Name Vitamin D3 receptor (VDR)
Synonyms Vitamin D(3) receptor; Nuclear vitamin D receptor; Nuclear receptor subfamily 1 group I member 1; NR1I1; 1,25-dihydroxyvitamin D3 receptor
Target Type Successful Target
Gene Name VDR
Biochemical Class Nuclear hormone receptor
UniProt ID
VDR_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Calcipotriol Ligand Info
Structure Description Crystal structure of VDR ligand binding domain complexed to calcipotriol. PDB:1S19
Method X-ray diffraction Resolution 2.10 Å Mutation No [1]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Residue
Distance (Å)
TYR143
2.768
TYR147
3.839
PHE150
4.197
LEU227
3.503
LEU230
4.052
ALA231
3.953
LEU233
3.665
VAL234
3.649
SER237
2.791
ILE268
4.437
ILE271
3.740
MET272
4.230
ARG274
2.839
SER275
3.406
Residue
Distance (Å)
SER278
2.932
TRP286
3.383
CYS288
3.550
TYR295
3.866
VAL300
3.769
HIS305
2.768
LEU309
3.531
LEU313
3.959
HIS397
2.738
TYR401
4.997
LEU414
4.287
VAL418
4.541
PHE422
4.589
Ligand Name: Calcitriol Ligand Info
Structure Description Crystal Structure Of The Nuclear Receptor For Vitamin D Ligand Binding Domain Bound to MC1288 PDB:1IE9
Method X-ray diffraction Resolution 1.40 Å Mutation No [2]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGGSVT
218

LELSQLSMLP
228
HLADLVSYSI
238
QKVIGFAKMI
248
PGFRDLTSED
258
QIVLLKSSAI
268

EVIMLRSNES
278
FTMDDMSWTC
288
GNQDYKYRVS
298
DVTKAGHSLE
308
LIEPLIKFQV
318

GLKKLNLHEE
328
EHVLLMAICI
338
VSPDRPGVQD
348
AALIEAIQDR
358
LSNTLQTYIR
368

CRHPPPGSHL
378
LYAKMIQKLA
388
DLRSLNEEHS
398
KQYRCLSFQP
408
ECSMKLTPLV
418

LEVFG
Residue
Distance (Å)
TYR143
2.776
TYR147
3.661
PHE150
4.136
LEU227
3.418
LEU230
3.885
LEU233
3.605
VAL234
3.598
SER237
2.809
ILE268
4.206
ILE271
3.883
MET272
4.137
ARG274
2.949
SER275
3.416
SER278
2.872
Residue
Distance (Å)
TRP286
3.403
CYS288
3.658
TYR295
4.035
VAL300
3.874
ALA303
4.783
HIS305
2.765
LEU309
4.123
LEU313
3.951
HIS397
2.823
TYR401
4.135
LEU404
4.409
LEU414
4.902
VAL418
4.191
PHE422
4.559
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Maxacalcitol Ligand Info
Structure Description Human VDR ligand binding domain in complex with maxacalcitol PDB:3B0T
Method X-ray diffraction Resolution 1.30 Å Mutation No [3]
PDB Sequence
ALRPKLSEEQ
128
QRIIAILLDA
138
HHKTYDPTYS
148
DFCQFRPPVR
158
VNDGGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MCZ or .MCZ2 or .MCZ3 or :3MCZ;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.804
TYR147
3.883
PHE150
4.197
LEU227
3.480
LEU230
4.108
ALA231
4.965
LEU233
3.832
VAL234
3.599
SER237
2.804
ILE268
4.451
ILE271
3.720
MET272
4.301
ARG274
2.967
SER275
3.375
SER278
2.817
Residue
Distance (Å)
TRP286
3.310
CYS288
3.627
TYR295
4.069
VAL300
3.673
ALA303
4.745
HIS305
2.797
LEU309
3.671
LEU313
3.949
HIS397
2.835
TYR401
4.036
LEU404
4.485
LEU414
4.932
VAL418
4.020
PHE422
4.444
Ligand Name: Seocalcitol Ligand Info
Structure Description Crystal structure of the VDR LBD complexed to seocalcitol. PDB:1S0Z
Method X-ray diffraction Resolution 2.50 Å Mutation No [1]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EB1 or .EB12 or .EB13 or :3EB1;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
3.034
TYR147
3.993
PHE150
4.147
LEU227
3.223
LEU230
4.047
ALA231
3.533
LEU233
3.647
VAL234
3.877
SER237
2.768
ILE268
4.333
ILE271
3.651
MET272
4.099
ARG274
2.855
SER275
3.393
Residue
Distance (Å)
SER278
2.849
TRP286
3.500
CYS288
3.649
TYR295
3.862
VAL300
3.838
HIS305
2.876
LEU309
3.569
LEU313
3.791
HIS397
2.929
TYR401
3.891
LEU404
4.212
LEU414
3.591
VAL418
3.990
PHE422
3.190
Ligand Name: Inecalcitol Ligand Info
Structure Description Crystal structure of the vdr ligand binding domain complexed to TX522 PDB:1TXI
Method X-ray diffraction Resolution 1.90 Å Mutation No [4]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TX5 or .TX52 or .TX53 or :3TX5;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.794
TYR147
3.791
PHE150
4.074
LEU227
3.601
LEU230
4.285
LEU233
4.053
VAL234
3.894
SER237
2.700
ILE268
3.809
ILE271
4.400
MET272
4.152
ARG274
2.796
SER275
3.469
SER278
2.883
Residue
Distance (Å)
TRP286
3.404
CYS288
3.639
TYR295
3.865
VAL300
3.681
ALA303
4.926
HIS305
2.823
LEU309
3.823
LEU313
4.047
HIS397
2.837
TYR401
3.985
LEU404
4.596
LEU414
4.741
VAL418
4.101
PHE422
4.315
Ligand Name: Lexacalcitol Ligand Info
Structure Description Crystal Structure Of The Nuclear Receptor For Vitamin D Ligand Binding Domain Bound to KH1060 PDB:1IE8
Method X-ray diffraction Resolution 1.52 Å Mutation No [2]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPLLYAKM
383
IQKLADLRSL
393
NEEHSKQYRC
403
LSFQPECSMK
413
LTPLVLEVFG
423
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KH1 or .KH12 or .KH13 or :3KH1;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.813
TYR147
3.797
PHE150
4.151
LEU227
3.438
LEU230
3.891
ALA231
3.701
LEU233
3.730
VAL234
3.582
SER237
2.754
ILE268
4.759
ILE271
3.826
MET272
4.171
ARG274
2.951
SER275
3.337
SER278
2.835
Residue
Distance (Å)
TRP286
3.459
CYS288
3.665
TYR295
4.000
VAL300
3.740
ALA303
3.442
HIS305
2.853
LEU309
3.816
LEU313
4.029
HIS397
2.624
TYR401
4.415
LEU404
3.389
LEU414
4.541
VAL418
3.956
PHE422
4.357
Ligand Name: (1r,3s,5z)-5-{(2e)-2-[(3ar,7as)-7a-(7-Hydroxy-7-Methyloctyl)octahydro-4h-Inden-4-Ylidene]ethylidene}-4-Methylidenecyclohexane-1,3-Diol Ligand Info
Structure Description Synthesis, Structure, and Biological Activity of des-Side Chain Analogues of 1alpha,25-Dihydroxyvitamin D3 with Substituents at C-18 PDB:3P8X
Method X-ray diffraction Resolution 1.70 Å Mutation No [5]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGGSVT
218

LELSQLSMLP
228
HLADLVSYSI
238
QKVIGFAKMI
248
PGFRDLTSED
258
QIVLLKSSAI
268

EVIMLRSNES
278
FTMDDMSWTC
288
GNQDYKYRVS
298
DVTKAGHSLE
308
LIEPLIKFQV
318

GLKKLNLHEE
328
EHVLLMAICI
338
VSPDRPGVQD
348
AALIEAIQDR
358
LSNTLQTYIR
368

CRHPPPGSHL
378
LYAKMIQKLA
388
DLRSLNEEHS
398
KQYRCLSFQP
408
ECSMKLTPLV
418

LEVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ZYD or .ZYD2 or .ZYD3 or :3ZYD;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.815
TYR147
3.782
PHE150
4.136
LEU227
3.807
LEU230
3.609
ALA231
4.686
LEU233
3.667
VAL234
3.642
SER237
2.843
ILE268
4.514
ILE271
3.657
MET272
4.248
ARG274
2.897
SER275
3.337
Residue
Distance (Å)
SER278
2.787
TRP286
3.393
CYS288
3.538
TYR295
4.032
VAL300
3.593
ALA303
4.409
HIS305
2.753
LEU313
3.734
HIS397
2.800
TYR401
4.023
LEU404
3.739
LEU414
3.669
VAL418
3.781
PHE422
3.696
Ligand Name: (1s,2s,3r,5z,7e,14beta,17alpha,23r)-23-(2-Hydroxy-2-Methylpropyl)-2-Methyl-20,24-Epoxy-9,10-Secochola-5,7,10-Triene-1,3-Diol Ligand Info
Structure Description Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277B(C23R) PDB:3A40
Method X-ray diffraction Resolution 1.45 Å Mutation No [6]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGGSVT
218

LELSQLSMLP
228
HLADLVSYSI
238
QKVIGFAKMI
248
PGFRDLTSED
258
QIVLLKSSAI
268

EVIMLRSNES
278
FTMDDMSWTC
288
GNQDYKYRVS
298
DVTKAGHSLE
308
LIEPLIKFQV
318

GLKKLNLHEE
328
EHVLLMAICI
338
VSPDRPGVQD
348
AALIEAIQDR
358
LSNTLQTYIR
368

CRHPPPGSHL
378
LYAKMIQKLA
388
DLRSLNEEHS
398
KQYRCLSFQP
408
ECSMKLTPLV
418

LEVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .23R or .23R2 or .23R3 or :323R;style chemicals stick;color identity;select .X:143 or .X:147 or .X:150 or .X:227 or .X:230 or .X:231 or .X:233 or .X:234 or .X:236 or .X:237 or .X:268 or .X:271 or .X:272 or .X:274 or .X:275 or .X:278 or .X:286 or .X:288 or .X:295 or .X:300 or .X:303 or .X:305 or .X:309 or .X:313 or .X:397 or .X:401 or .X:404 or .X:418 or .X:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.802
TYR147
3.803
PHE150
3.706
LEU227
3.574
LEU230
3.788
ALA231
4.921
LEU233
3.932
VAL234
3.732
TYR236
4.629
SER237
2.788
ILE268
4.418
ILE271
3.893
MET272
4.298
ARG274
2.954
SER275
3.389
Residue
Distance (Å)
SER278
2.838
TRP286
3.547
CYS288
3.676
TYR295
3.810
VAL300
3.837
ALA303
4.337
HIS305
2.809
LEU309
3.953
LEU313
4.029
HIS397
2.809
TYR401
4.056
LEU404
4.378
VAL418
4.683
PHE422
4.815
Ligand Name: (1s,2s,3r,5z,7e,14beta,17alpha)-17-[(2s,4s)-4-(2-Hydroxy-2-Methylpropyl)-2-Methyltetrahydrofuran-2-Yl]-2-Methyl-9,10-Secoandrosta-5,7,10-Triene-1,3-Diol Ligand Info
Structure Description Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277A(C23S) PDB:3A3Z
Method X-ray diffraction Resolution 1.72 Å Mutation No [6]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGGSVT
218

LELSQLSMLP
228
HLADLVSYSI
238
QKVIGFAKMI
248
PGFRDLTSED
258
QIVLLKSSAI
268

EVIMLRSNES
278
FTMDDMSWTC
288
GNQDYKYRVS
298
DVTKAGHSLE
308
LIEPLIKFQV
318

GLKKLNLHEE
328
EHVLLMAICI
338
VSPDRPGVQD
348
AALIEAIQDR
358
LSNTLQTYIR
368

CRHPPPGSHL
378
LYAKMIQKLA
388
DLRSLNEEHS
398
KQYRCLSFQP
408
ECSMKLTPLV
418

LEVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2MV or .2MV2 or .2MV3 or :32MV;style chemicals stick;color identity;select .X:143 or .X:147 or .X:150 or .X:227 or .X:230 or .X:231 or .X:233 or .X:234 or .X:236 or .X:237 or .X:268 or .X:271 or .X:272 or .X:274 or .X:275 or .X:278 or .X:286 or .X:288 or .X:295 or .X:300 or .X:303 or .X:305 or .X:309 or .X:313 or .X:397 or .X:401 or .X:404 or .X:414 or .X:418 or .X:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.828
TYR147
3.833
PHE150
3.836
LEU227
3.529
LEU230
3.837
ALA231
4.835
LEU233
3.974
VAL234
3.654
TYR236
4.673
SER237
2.774
ILE268
4.373
ILE271
3.721
MET272
4.308
ARG274
2.973
SER275
3.427
Residue
Distance (Å)
SER278
2.814
TRP286
3.628
CYS288
3.651
TYR295
3.973
VAL300
3.848
ALA303
4.286
HIS305
2.806
LEU309
3.855
LEU313
3.970
HIS397
2.838
TYR401
4.205
LEU404
4.345
LEU414
4.611
VAL418
4.331
PHE422
4.812
Ligand Name: (1S,3R,5Z,7E,14beta,17alpha,23R)-23-(2-hydroxy-2-methylpropyl)-20,24-epoxy-9,10-secochola-5,7,10-triene-1,3-diol Ligand Info
Structure Description Structure-based design of a superagonist ligand for the vitamin D nuclear receptor PDB:3CS6
Method X-ray diffraction Resolution 1.80 Å Mutation No [7]
PDB Sequence
SLRPKLSEEQ
128
QRIIAILLDA
138
HHKTYDPTYS
148
DFCQFRPPVR
158
VNDGGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0CO or .0CO2 or .0CO3 or :30CO;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.781
TYR147
3.662
PHE150
4.059
LEU227
3.451
LEU230
3.769
ALA231
4.774
LEU233
3.701
VAL234
3.691
SER237
2.719
ILE268
4.317
ILE271
3.734
MET272
4.351
ARG274
2.886
SER275
3.347
Residue
Distance (Å)
SER278
2.804
TRP286
3.493
CYS288
3.613
TYR295
3.806
VAL300
3.882
ALA303
4.375
HIS305
3.012
LEU309
3.779
LEU313
4.006
HIS397
2.984
TYR401
3.928
LEU404
4.144
VAL418
4.686
PHE422
4.759
Ligand Name: 2alpha-(3-Hydroxypropyl)-1alpha,25-dihydroxyvitamin D3 Ligand Info
Structure Description Crystal structure of VDR LBD in complex with 2alpha(3-hydroxy-1-propyl) calcitriol PDB:2HB7
Method X-ray diffraction Resolution 1.80 Å Mutation No [8]
PDB Sequence
SLRPKLSEEQ
128
QRIIAILLDA
138
HHKTYDPTYS
148
DFCQFRPPVR
158
VNDGGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .O1C or .O1C2 or .O1C3 or :3O1C;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:277 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.637
TYR143
2.768
ASP144
3.921
TYR147
3.768
PHE150
3.752
LEU227
3.468
LEU230
3.931
LEU233
3.720
VAL234
3.546
TYR236
3.831
SER237
2.969
LYS240
4.190
ILE268
4.301
ILE271
3.701
MET272
4.310
ARG274
2.857
SER275
3.359
Residue
Distance (Å)
GLU277
4.990
SER278
2.809
TRP286
3.558
CYS288
3.646
TYR295
3.896
VAL300
3.813
ALA303
4.840
HIS305
2.794
LEU309
3.718
LEU313
3.968
HIS397
2.777
TYR401
4.085
LEU404
4.215
LEU414
4.496
VAL418
3.850
PHE422
4.349
Ligand Name: (1s,3s,5z,7e,14beta,17alpha)-9,10-Secocholesta-5,7,10-Triene-1,3,25-Triol Ligand Info
Structure Description Crystal structure of the human VDR ligand binding domain bound to the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3 PDB:3A78
Method X-ray diffraction Resolution 1.90 Å Mutation No [9]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGGSVT
218

LELSQLSMLP
228
HLADLVSYSI
238
QKVIGFAKMI
248
PGFRDLTSED
258
QIVLLKSSAI
268

EVIMLRSNES
278
FTMDDMSWTC
288
GNQDYKYRVS
298
DVTKAGHSLE
308
LIEPLIKFQV
318

GLKKLNLHEE
328
EHVLLMAICI
338
VSPDRPGVQD
348
AALIEAIQDR
358
LSNTLQTYIR
368

CRHPPPGSHL
378
LYAKMIQKLA
388
DLRSLNEEHS
398
KQYRCLSFQP
408
ECSMKLTPLV
418

LEVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3EV or .3EV2 or .3EV3 or :33EV;style chemicals stick;color identity;select .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:277 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
3.028
ASP144
4.831
TYR147
3.365
PHE150
3.767
LEU227
3.428
LEU230
3.848
LEU233
3.702
VAL234
3.565
SER237
2.709
ILE268
4.332
ILE271
3.677
MET272
4.288
ARG274
3.092
SER275
3.346
GLU277
4.880
Residue
Distance (Å)
SER278
3.629
TRP286
3.414
CYS288
3.639
TYR295
3.926
VAL300
3.723
ALA303
4.666
HIS305
2.673
LEU309
3.868
LEU313
3.955
HIS397
2.724
TYR401
4.037
LEU404
4.209
LEU414
4.627
VAL418
4.012
PHE422
4.580
Ligand Name: 1alpha,25-dihydroxy-2alpha-(3-hydroxypropoxy)vitamin D3 Ligand Info
Structure Description Crystal structure of VDR LBD in complex with 2 alpha-(3-hydroxy-1-propoxy) calcitriol PDB:2HAR
Method X-ray diffraction Resolution 1.90 Å Mutation No [8]
PDB Sequence
SLRPKLSEEQ
128
QRIIAILLDA
138
HHKTYDPTYS
148
DFCQFRPPVR
158
VNDGGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPGSHLLYA
381
KMIQKLADLR
391
SLNEEHSKQY
401
RCLSFQPECS
411
MKLTPLVLEV
421

FG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OCC or .OCC2 or .OCC3 or :3OCC;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.310
TYR143
2.717
ASP144
3.647
TYR147
3.808
PHE150
3.620
LEU227
3.543
LEU230
3.996
LEU233
3.560
VAL234
3.519
TYR236
3.812
SER237
2.924
LYS240
3.980
ILE268
4.102
ILE271
3.620
MET272
4.262
ARG274
2.879
Residue
Distance (Å)
SER275
3.334
SER278
2.780
TRP286
3.455
CYS288
3.509
TYR295
3.935
VAL300
3.700
HIS305
2.752
LEU309
3.632
LEU313
3.882
HIS397
2.742
TYR401
4.006
LEU404
4.390
LEU414
4.486
VAL418
3.803
PHE422
4.210
Ligand Name: 2alpha-Propyl-1alpha,25-dihydroxyvitamin D3 Ligand Info
Structure Description Crystal structure of VDR LBD complexed to 2alpha-propyl-calcitriol PDB:2HAM
Method X-ray diffraction Resolution 1.90 Å Mutation No [8]
PDB Sequence
SLRPKLSEEQ
128
QRIIAILLDA
138
HHKTYDPTYS
148
DFCQFRPPVR
158
VNDGGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .C33 or .C332 or .C333 or :3C33;style chemicals stick;color identity;select .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.749
ASP144
3.701
TYR147
3.677
PHE150
3.832
LEU227
3.488
LEU230
3.986
LEU233
3.742
VAL234
3.557
TYR236
4.210
SER237
2.828
ILE268
4.204
ILE271
3.812
MET272
4.310
ARG274
2.913
SER275
3.329
Residue
Distance (Å)
SER278
2.753
TRP286
3.441
CYS288
3.558
TYR295
3.896
VAL300
3.705
HIS305
2.681
LEU309
3.685
LEU313
3.915
HIS397
2.748
TYR401
4.085
LEU404
4.354
LEU414
4.574
VAL418
3.857
PHE422
4.053
Ligand Name: (1r,3r)-5-[(2z)-2-[(1r,3as,7ar)-7a-Methyl-1-[(2r)-6-Methyl-6-Oxidanyl-Heptan-2-Yl]-2,3,3a,5,6,7-Hexahydro-1h-Inden-4-Ylidene]ethylidene]cyclohexane-1,3-Diol Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-1a,25-Dihydroxy-19-norvitamin D3 PDB:3X36
Method X-ray diffraction Resolution 1.93 Å Mutation No [10]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .41W or .41W2 or .41W3 or :341W;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.960
TYR147
3.947
PHE150
4.077
LEU227
3.454
LEU230
4.224
LEU233
4.047
VAL234
3.954
SER237
2.755
ILE268
4.360
ILE271
3.949
MET272
4.346
ARG274
2.833
SER275
3.335
SER278
2.685
Residue
Distance (Å)
TRP286
3.297
CYS288
3.868
TYR295
3.994
VAL300
3.570
ALA303
4.333
HIS305
2.760
LEU309
3.962
LEU313
4.103
HIS397
2.691
TYR401
4.078
LEU404
4.050
LEU414
4.434
VAL418
4.213
PHE422
4.697
Ligand Name: 2alpha-Propoxy-1alpha,25-dihydroxyvitamin D3 Ligand Info
Structure Description Crystal structure of VDR LBD in complex with 2alpha-(1-propoxy) calcitriol PDB:2HAS
Method X-ray diffraction Resolution 1.96 Å Mutation No [8]
PDB Sequence
SLRPKLSEEQ
128
QRIIAILLDA
138
HHKTYDPTYS
148
DFCQFRPPVR
158
VNDGGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .C3O or .C3O2 or .C3O3 or :3C3O;style chemicals stick;color identity;select .A:143 or .A:144 or .A:145 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.780
ASP144
3.247
PRO145
4.994
TYR147
3.576
PHE150
3.637
LEU227
3.550
LEU230
4.153
LEU233
3.690
VAL234
3.592
TYR236
3.943
SER237
2.841
ILE268
4.121
ILE271
3.737
MET272
4.299
ARG274
2.825
Residue
Distance (Å)
SER275
3.344
SER278
2.741
TRP286
3.481
CYS288
3.539
TYR295
3.994
VAL300
3.683
HIS305
2.784
LEU309
3.545
LEU313
3.927
HIS397
2.727
TYR401
3.940
LEU404
4.361
LEU414
4.625
VAL418
3.771
PHE422
4.249
Ligand Name: (1S,3R,5Z,7E,14beta,17alpha)-17-[(2S,4S)-4-(2-hydroxy-2-methylpropyl)-2-methyltetrahydrofuran-2-yl]-9,10-secoandrosta-5,7,10-triene-1,3-diol Ligand Info
Structure Description Structure-based design of a superagonist ligand for the vitamin D nuclear receptor PDB:3CS4
Method X-ray diffraction Resolution 2.00 Å Mutation No [7]
PDB Sequence
SLRPKLSEEQ
128
QRIIAILLDA
138
HHKTYDPTYS
148
DFCQFRPPVR
158
VNDGGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .COV or .COV2 or .COV3 or :3COV;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.756
TYR147
3.747
PHE150
4.223
LEU227
3.424
LEU230
3.842
ALA231
4.898
LEU233
3.786
VAL234
3.568
SER237
2.735
ILE268
4.253
ILE271
3.760
MET272
4.332
ARG274
2.882
SER275
3.340
SER278
2.860
Residue
Distance (Å)
TRP286
3.463
CYS288
3.592
TYR295
3.948
VAL300
3.612
ALA303
4.366
HIS305
2.802
LEU309
3.663
LEU313
3.985
HIS397
2.787
TYR401
4.135
LEU404
4.131
LEU414
4.594
VAL418
4.178
PHE422
4.564
Ligand Name: 2alpha-Methyl-1alpha,25-dihydroxy-vitamin D3 Ligand Info
Structure Description Crystal structure of VDR LBD in complex with 2alpha-methyl calcitriol PDB:2HB8
Method X-ray diffraction Resolution 2.00 Å Mutation No [8]
PDB Sequence
SLRPKLSEEQ
128
QRIIAILLDA
138
HHKTYDPTYS
148
DFCQFRPPVR
158
VNDGGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MVD or .MVD2 or .MVD3 or :3MVD;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.804
TYR147
3.741
PHE150
3.877
LEU227
3.482
LEU230
3.883
LEU233
3.792
VAL234
3.523
TYR236
4.577
SER237
2.749
ILE268
4.269
ILE271
3.746
MET272
4.246
ARG274
2.881
SER275
3.390
SER278
2.821
Residue
Distance (Å)
TRP286
3.470
CYS288
3.529
TYR295
3.917
VAL300
3.777
ALA303
4.780
HIS305
2.747
LEU309
3.630
LEU313
3.887
HIS397
2.839
TYR401
4.060
LEU404
4.299
LEU414
4.628
VAL418
3.998
PHE422
4.359
Ligand Name: (1r,3r,7z,14beta,17alpha)-17-[(2r)-6-Hydroxy-6-Methylheptan-2-Yl]-9,10-Secoestra-5,7-Diene-1,3-Diol Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-14-epi-1a,25-Dihydroxy-19-norvitamin D3 PDB:3X31
Method X-ray diffraction Resolution 2.11 Å Mutation No [11]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .41V or .41V2 or .41V3 or :341V;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.907
TYR147
4.091
PHE150
4.072
LEU227
3.543
LEU230
4.225
LEU233
4.003
VAL234
3.673
SER237
3.148
ILE268
3.900
ILE271
3.912
MET272
4.161
ARG274
2.864
SER275
3.355
SER278
2.706
Residue
Distance (Å)
TRP286
3.300
CYS288
3.745
TYR295
3.936
VAL300
3.672
ALA303
4.513
HIS305
2.623
LEU309
3.822
LEU313
4.083
HIS397
2.763
TYR401
4.217
LEU404
3.728
VAL418
4.801
PHE422
4.606
Ligand Name: (1r,2s,3r)-5-[2-[(1r,3as,7ar)-1-[(2r)-6-Hydroxy-6-Methyl-Heptan-2-Yl]-7a-Methyl-1,2,3,3a,6,7-Hexahydroinden-4-Yl]ethynyl]-2-Methyl-Cyclohex-4-Ene-1,3-Diol Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with Yne-diene type analog of active 14-epi-2beta-methyl-19-norvitamin D3 PDB:3AUR
Method X-ray diffraction Resolution 2.21 Å Mutation No [12]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CA9 or .CA92 or .CA93 or :3CA9;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:277 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.742
TYR147
3.791
PHE150
3.843
LEU227
3.428
LEU230
4.225
LEU233
3.597
VAL234
3.977
TYR236
4.531
SER237
2.797
ILE268
3.954
ILE271
4.181
MET272
4.010
ARG274
2.869
SER275
3.389
GLU277
4.894
Residue
Distance (Å)
SER278
2.811
TRP286
3.637
CYS288
3.714
TYR295
4.156
VAL300
3.610
ALA303
4.580
HIS305
2.674
LEU309
3.745
LEU313
3.865
HIS397
2.626
TYR401
3.841
LEU404
4.052
LEU414
4.602
VAL418
4.133
PHE422
4.546
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Methyl (1s,3e)-3-{(2r)-2-[(1r,3as,4e,7ar)-4-{(2z)-2-[(3r,4s,5r)-3,5-Dihydroxy-4-(3-Hydroxypropoxy)-2-Methylidenecyclohexylidene]ethylidene}-7a-Methyloctahydro-1h-Inden-1-Yl]propylidene}-1-Ethyl-2-Oxocyclopentanecarboxylate (Non-Preferred Name) Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with 4-MP PDB:3VHW
Method X-ray diffraction Resolution 2.43 Å Mutation No [13]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .VHW or .VHW2 or .VHW3 or :3VHW;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.209
TYR143
2.635
ASP144
3.769
TYR147
3.948
PHE150
3.647
LEU227
3.394
LEU230
4.009
ALA231
3.649
LEU233
3.492
VAL234
3.654
TYR236
3.362
SER237
2.773
LYS240
3.917
ILE268
3.640
ILE271
3.794
MET272
4.235
ARG274
2.889
Residue
Distance (Å)
SER275
3.417
SER278
2.632
TRP286
3.529
CYS288
3.413
TYR295
4.139
VAL300
3.766
ALA303
3.900
HIS305
3.319
LEU309
3.535
LEU313
3.725
HIS397
2.794
TYR401
3.977
LEU404
3.618
LEU414
4.677
VAL418
3.634
PHE422
3.765
Ligand Name: (1r,2s,3s,5z)-5-[(2e)-2-[(1r,3as,7ar)-7a-Methyl-1-[(2r)-6-Methyl-6-Oxidanyl-Heptan-2-Yl]-2,3,3a,5,6,7-Hexahydro-1h-Inden-4-Ylidene]ethylidene]-4-Methylidene-2-[2-(1,2,3,4-Tetrazol-2-Yl)ethyl]cyclohexane-1,3-Diol Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(2H-tetrazol-2-yl)ethyl]vitamin D3 PDB:4ITE
Method X-ray diffraction Resolution 2.49 Å Mutation No [14]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TEY or .TEY2 or .TEY3 or :3TEY;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:145 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.936
TYR143
2.935
ASP144
2.848
PRO145
4.687
TYR147
3.345
PHE150
3.687
LEU227
3.434
LEU230
4.063
LEU233
3.436
VAL234
3.629
TYR236
3.691
SER237
2.745
LYS240
4.353
ILE268
4.218
ILE271
3.718
MET272
4.328
Residue
Distance (Å)
ARG274
2.929
SER275
3.259
SER278
2.708
TRP286
3.416
CYS288
3.556
TYR295
4.138
VAL300
3.778
HIS305
2.794
LEU309
3.589
LEU313
3.963
HIS397
2.727
TYR401
3.902
LEU404
4.104
LEU414
4.731
VAL418
3.804
PHE422
4.140
Ligand Name: (1r,3s,5z)-5-[(2e)-2-[(1r,3s,3as,7ar)-1-[(2r)-6-Hydroxy-6-Methyl-Heptan-2-Yl]-3-Methoxy-7a-Methyl-2,3,3a,5,6,7-Hexahydro-1h-Inden-4-Ylidene]ethylidene]-4-Methylidene-Cyclohexane-1,3-Diol Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with 15alpha-methoxy-1alpha,25-dihydroxyvitamin D3 PDB:3AX8
Method X-ray diffraction Resolution 2.60 Å Mutation No [15]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EIM or .EIM2 or .EIM3 or :3EIM;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:317 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.982
TYR147
4.028
PHE150
4.152
LEU227
3.301
LEU230
4.091
ALA231
4.978
LEU233
3.756
VAL234
3.600
SER237
2.729
ILE268
4.147
ILE271
3.834
MET272
3.626
ARG274
2.767
SER275
2.939
SER278
2.603
Residue
Distance (Å)
TRP286
3.299
CYS288
3.676
TYR295
4.076
VAL300
3.841
ALA303
4.976
HIS305
2.638
LEU309
3.865
LEU313
3.433
GLN317
3.935
HIS397
2.922
TYR401
3.771
LEU404
3.995
LEU414
4.328
VAL418
3.648
PHE422
4.194
Ligand Name: (1s,3r,5z,7e,20s,23s)-1,3-Dihydroxy-23,26-Epoxy-9,10-Secocholesta-5,7,10,25(27)-Tetraen-26-One Ligand Info
Structure Description Crystal structure of the human vitamin D receptor (H305F/H397F) ligand binding domain complexed with TEI-9647 PDB:3A2J
Method X-ray diffraction Resolution 2.70 Å Mutation Yes [16]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGFSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEFSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TEJ or .TEJ2 or .TEJ3 or :3TEJ;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.919
TYR147
3.912
PHE150
4.043
LEU227
3.544
LEU230
3.642
ALA231
3.498
LEU233
3.947
VAL234
3.668
SER237
2.813
ILE268
4.367
ILE271
3.682
MET272
3.856
ARG274
3.037
SER275
3.359
Residue
Distance (Å)
SER278
2.692
TRP286
3.580
CYS288
3.600
TYR295
4.232
VAL300
3.637
ALA303
4.888
PHE305
3.525
LEU309
4.079
LEU313
3.833
PHE397
3.165
LEU414
4.869
VAL418
4.398
PHE422
4.151
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: (1r,2s,3s,5z)-5-[(2e)-2-[(1r,3as,7ar)-7a-Methyl-1-[(2r)-6-Methyl-6-Oxidanyl-Heptan-2-Yl]-2,3,3a,5,6,7-Hexahydro-1h-Inden-4-Ylidene]ethylidene]-4-Methylidene-2-[2-(1,2,3,4-Tetrazol-1-Yl)ethyl]cyclohexane-1,3-Diol Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(1H-tetrazole-1-yl)ethyl]vitamin D3 PDB:4ITF
Method X-ray diffraction Resolution 2.84 Å Mutation No [14]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TFY or .TFY2 or .TFY3 or :3TFY;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:145 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:277 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.630
TYR143
2.828
ASP144
2.973
PRO145
4.903
TYR147
3.728
PHE150
3.950
LEU227
3.465
LEU230
4.237
LEU233
3.505
VAL234
3.688
TYR236
3.439
SER237
3.124
LYS240
3.872
ILE268
4.190
ILE271
3.584
MET272
4.166
ARG274
2.874
Residue
Distance (Å)
SER275
3.279
GLU277
4.943
SER278
2.692
TRP286
3.493
CYS288
3.503
TYR295
4.161
VAL300
3.745
ALA303
4.769
HIS305
2.882
LEU309
3.634
LEU313
3.774
HIS397
2.985
TYR401
4.004
LEU404
4.096
LEU414
4.383
VAL418
3.754
PHE422
4.464
Ligand Name: 1-({[(1r,2s,3r,5z,7e,14beta,17alpha)-1,3,25-Trihydroxy-9,10-Secocholesta-5,7,10-Trien-2-Yl]oxy}methyl)cyclopropanecarbonitrile Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1-((((1S,2R,6R,Z)-2,6-dihydroxy-4-((E)-2-((1R,3aS,7aR)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methylhexahydro-1H-inden-4(2H)-ylidene)ethylidene)-3-methylenecyclohexyl)oxy)methyl)cyclopropanecarbonitrile PDB:3WWR
Method X-ray diffraction Resolution 3.18 Å Mutation No [17]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3AJ or .3AJ2 or .3AJ3 or :33AJ;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:145 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.755
TYR143
3.671
ASP144
3.100
PRO145
4.998
TYR147
3.707
PHE150
4.079
LEU227
3.671
LEU230
4.253
ALA231
4.753
LEU233
4.126
VAL234
3.574
TYR236
3.770
SER237
3.452
LYS240
3.868
ILE268
4.351
ILE271
3.557
MET272
4.359
Residue
Distance (Å)
ARG274
2.863
SER275
3.336
SER278
2.490
TRP286
3.764
CYS288
3.507
TYR295
4.460
VAL300
3.984
ALA303
4.807
HIS305
3.655
LEU309
4.182
LEU313
3.988
HIS397
2.659
TYR401
4.333
LEU404
4.296
LEU414
4.485
VAL418
3.920
PHE422
4.368
Ligand Name: (1s,3r,5z,7e,14beta,17alpha,20s)-20-[5-(1-Hydroxy-1-Methylethyl)furan-2-Yl]-9,10-Secopregna-5,7,10-Triene-1,3-Diol Ligand Info
Structure Description Design, Chemical synthesis, Functional characterization and Crystal structure of the sidechain analogue of 1,25-dihydroxyvitamin D3. PDB:3OGT
Method X-ray diffraction Resolution 1.75 Å Mutation No [18]
PDB Sequence
SLRPKLSEEQ
128
QRIIAILLDA
138
HHKTYDPTYS
148
DFCQFRPPVR
158
VNDGGGSVTL
219

ELSQLSMLPH
229
LADLVSYSIQ
239
KVIGFAKMIP
249
GFRDLTSEDQ
259
IVLLKSSAIE
269

VIMLRSNESF
279
TMDDMSWTCG
289
NQDYKYRVSD
299
VTKAGHSLEL
309
IEPLIKFQVG
319

LKKLNLHEEE
329
HVLLMAICIV
339
SPDRPGVQDA
349
ALIEAIQDRL
359
SNTLQTYIRC
369

RHPPPGSHLL
379
YAKMIQKLAD
389
LRSLNEEHSK
399
QYRCLSFQPE
409
CSMKLTPLVL
419

EVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FMV or .FMV2 or .FMV3 or :3FMV;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.872
TYR147
3.902
PHE150
4.272
LEU227
3.758
LEU230
4.095
ALA231
4.958
LEU233
3.945
VAL234
3.555
SER237
2.731
ILE268
3.505
ILE271
3.709
MET272
4.366
ARG274
2.974
SER275
3.369
Residue
Distance (Å)
SER278
2.771
TRP286
3.551
CYS288
3.594
TYR295
4.155
VAL300
3.685
ALA303
4.907
HIS305
2.837
LEU309
3.714
LEU313
3.991
HIS397
2.811
TYR401
4.102
LEU404
4.555
VAL418
4.265
PHE422
4.421
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: (3e,5e)-6-(3-{2-[3,4-Bis(Hydroxymethyl)phenyl]ethyl}phenyl)-1,1,1-Trifluoro-2-(Trifluoromethyl)octa-3,5-Dien-2-Ol Ligand Info
Structure Description Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor PDB:4G2I
Method X-ray diffraction Resolution 1.80 Å Mutation No [19]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0VQ or .0VQ2 or .0VQ3 or :30VQ;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:277 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:310 or .A:313 or .A:317 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.727
TYR147
3.627
PHE150
4.406
LEU227
3.224
LEU230
3.788
ALA231
3.705
LEU233
3.636
VAL234
3.321
SER237
2.670
ILE268
4.135
ILE271
3.858
MET272
3.949
ARG274
2.969
SER275
3.296
GLU277
4.909
SER278
2.800
Residue
Distance (Å)
TRP286
3.607
CYS288
3.888
TYR295
4.142
VAL300
3.674
ALA303
4.100
HIS305
2.770
LEU309
3.666
ILE310
4.973
LEU313
3.671
GLN317
4.893
HIS397
2.725
TYR401
3.525
LEU404
3.264
LEU414
3.688
VAL418
3.315
PHE422
3.258
Ligand Name: (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R)-6-hydroxy-6-(1,3-thiazol-2-yl)hexan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidenecyclohexane-1,3-diol Ligand Info
Structure Description Crystal structure of a novel vitamin D3 analogue, ZK203278 showing dissociated profile PDB:3KPZ
Method X-ray diffraction Resolution 1.90 Å Mutation No [20]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPGSHLLY
380
AKMIQKLADL
390
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ZNE or .ZNE2 or .ZNE3 or :3ZNE;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.745
TYR147
3.630
PHE150
4.095
LEU227
4.475
LEU230
3.842
ALA231
3.485
LEU233
3.680
VAL234
3.740
SER237
2.798
ILE268
4.900
ILE271
3.748
MET272
4.097
ARG274
2.804
SER275
3.338
Residue
Distance (Å)
SER278
2.774
TRP286
3.373
CYS288
3.546
TYR295
3.781
VAL300
3.997
HIS305
2.703
LEU309
3.938
LEU313
3.693
HIS397
2.718
TYR401
3.514
LEU404
4.654
LEU414
3.507
VAL418
3.033
PHE422
4.014
Ligand Name: 5-(3-{4-[(2S)-2-hydroxy-3,3-dimethylbutoxy]-3-methylphenyl}pentan-3-yl)-3-methyl-N-(1H-tetrazol-5-yl)thiophene-2-carboxamide Ligand Info
Structure Description Crystal structure of human vitamin D receptor ligand binding domain in complex with a VDRM PDB:5V39
Method X-ray diffraction Resolution 2.20 Å Mutation No [21]
PDB Sequence
PKLSEEQQRI
131
IAILLDAHHK
141
TYDPTYSDFC
151
QFRPPVRVND
161
GGGSVTLELL
222

QLSMLPHLAD
232
LVSYSIQKVI
242
GFAKMIPGFR
252
DLTSEDQIVL
262
LKSSAIEVIM
272

LRSNESFTMD
282
DMSWTCGNQD
292
YKYRVSDVTK
302
AGHSLELIEP
312
LIKFQVGLKK
322

LNLHEEEHVL
332
LMAICIVSPD
342
RPGVQDAALI
352
EAIQDRLSNT
362
LQTYIRCRHP
372

PPGSHLLYAK
382
MIQKLADLRS
392
LNEEHSKQYR
402
CLSFQPECSM
412
KLTPLVLEVF
422

G
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8VM or .8VM2 or .8VM3 or :38VM;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:236 or .A:237 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:305 or .A:309 or .A:313 or .A:317 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
3.430
TYR147
4.198
PHE150
3.924
LEU227
3.879
LEU230
3.897
ALA231
3.512
LEU233
3.434
VAL234
3.517
TYR236
3.781
SER237
2.887
ILE271
3.708
MET272
4.351
ARG274
2.891
SER275
3.482
SER278
3.444
Residue
Distance (Å)
TRP286
3.596
CYS288
3.483
TYR295
3.659
VAL300
3.761
HIS305
2.711
LEU309
3.874
LEU313
3.875
GLN317
4.790
HIS397
2.710
TYR401
4.060
LEU404
3.763
LEU414
4.072
VAL418
3.725
PHE422
3.721
Ligand Name: 4-{[(1r,2s,3r,5z,7e,14beta,17alpha)-1,3,25-Trihydroxy-9,10-Secocholesta-5,7,10-Trien-2-Yl]oxy}butanenitrile Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol PDB:5GT4
Method X-ray diffraction Resolution 1.83 Å Mutation No [22]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGGSVT
218

LELSQLSMLP
228
HLADLVSYSI
238
QKVIGFAKMI
248
PGFRDLTSED
258
QIVLLKSSAI
268

EVIMLRSNES
278
FTMDDMSWTC
288
GNQDYKYRVS
298
DVTKAGHSLE
308
LIEPLIKFQV
318

GLKKLNLHEE
328
EHVLLMAICI
338
VSPDRPGVQD
348
AALIEAIQDR
358
LSNTLQTYIR
368

CRHPPPGSHL
378
LYAKMIQKLA
388
DLRSLNEEHS
398
KQYRCLSFQP
408
ECSMKLTPLV
418

LEVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2KB or .2KB2 or .2KB3 or :32KB;style chemicals stick;color identity;select .A:143 or .A:144 or .A:145 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.874
ASP144
2.279
PRO145
4.020
TYR147
3.631
PHE150
3.667
LEU227
3.575
LEU230
4.036
LEU233
3.466
VAL234
3.627
TYR236
4.111
SER237
2.779
ILE268
4.222
ILE271
3.827
MET272
4.262
ARG274
2.901
Residue
Distance (Å)
SER275
3.348
SER278
2.695
TRP286
3.439
CYS288
3.715
TYR295
4.014
VAL300
3.727
HIS305
2.852
LEU309
3.853
LEU313
3.918
HIS397
2.704
TYR401
3.869
LEU404
4.217
LEU414
4.679
VAL418
3.893
PHE422
4.290
Ligand Name: (1R,2S,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]ethenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol PDB:5YT2
Method X-ray diffraction Resolution 2.00 Å Mutation No [23]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGGSVT
218

LELSQLSMLP
228
HLADLVSYSI
238
QKVIGFAKMI
248
PGFRDLTSED
258
QIVLLKSSAI
268

EVIMLRSNES
278
FTMDDMSWTC
288
GNQDYKYRVS
298
DVTKAGHSLE
308
LIEPLIKFQV
318

GLKKLNLHEE
328
EHVLLMAICI
338
VSPDRPGVQD
348
AALIEAIQDR
358
LSNTLQTYIR
368

CRHPPPGSHL
378
LYAKMIQKLA
388
DLRSLNEEHS
398
KQYRCLSFQP
408
ECSMKLTPLV
418

LEVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .90O or .90O2 or .90O3 or :390O;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.577
TYR143
2.832
ASP144
3.825
TYR147
3.956
PHE150
4.012
LEU227
3.498
LEU230
4.291
LEU233
3.636
VAL234
3.888
TYR236
3.762
SER237
2.785
LYS240
3.999
ILE268
3.982
ILE271
4.177
MET272
4.285
ARG274
2.927
Residue
Distance (Å)
SER275
3.371
SER278
2.899
TRP286
3.566
CYS288
3.890
TYR295
4.004
VAL300
3.576
ALA303
4.771
HIS305
2.750
LEU309
3.842
LEU313
3.947
HIS397
2.634
TYR401
4.137
LEU404
4.034
LEU414
4.745
VAL418
4.215
PHE422
4.175
Ligand Name: Thenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol Ligand Info
Structure Description Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2R,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol PDB:5YSY
Method X-ray diffraction Resolution 2.00 Å Mutation No [23]
PDB Sequence
DSLRPKLSEE
127
QQRIIAILLD
137
AHHKTYDPTY
147
SDFCQFRPPV
157
RVNDGGGSVT
218

LELSQLSMLP
228
HLADLVSYSI
238
QKVIGFAKMI
248
PGFRDLTSED
258
QIVLLKSSAI
268

EVIMLRSNES
278
FTMDDMSWTC
288
GNQDYKYRVS
298
DVTKAGHSLE
308
LIEPLIKFQV
318

GLKKLNLHEE
328
EHVLLMAICI
338
VSPDRPGVQD
348
AALIEAIQDR
358
LSNTLQTYIR
368

CRHPPPGSHL
378
LYAKMIQKLA
388
DLRSLNEEHS
398
KQYRCLSFQP
408
ECSMKLTPLV
418

LEVFG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .90L or .90L2 or .90L3 or :390L;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.539
TYR143
2.967
ASP144
3.604
TYR147
3.939
PHE150
3.848
LEU227
3.493
LEU230
4.174
LEU233
3.660
VAL234
3.778
TYR236
3.729
SER237
2.660
LYS240
4.171
ILE268
3.844
ILE271
4.014
MET272
4.242
ARG274
2.976
Residue
Distance (Å)
SER275
3.438
SER278
2.920
TRP286
3.695
CYS288
3.824
TYR295
3.903
VAL300
3.521
ALA303
4.875
HIS305
2.776
LEU309
3.776
LEU313
3.903
HIS397
2.757
TYR401
4.206
LEU404
4.217
VAL418
4.469
PHE422
4.264
Ligand Name: (4s)-4-Hydroxy-5-[4-(3-{4-[(3s)-3-Hydroxy-4,4-Dimethylpentyl]-3-Methylphenyl}pentan-3-Yl)-2-Methylphenoxy]pentanoic Acid Ligand Info
Structure Description Crystal Structure Analysis of Vitamin D receptor PDB:3AZ3
Method X-ray diffraction Resolution 1.36 Å Mutation No [24]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
390
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPLLYAKM
383
IQKLADLRSL
493
NEEHSKQYRC
403
LSFQPECSMK
413
LTPLVLEVFG
423
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DS6 or .DS62 or .DS63 or :3DS6;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:317 or .A:395 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422 or .A:497; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.703
TYR143
3.559
ASP144
4.873
TYR147
4.342
PHE150
3.874
LEU227
3.970
LEU230
3.989
ALA231
3.680
LEU233
3.574
VAL234
3.711
TYR236
3.963
SER237
2.846
LYS240
3.680
ILE271
3.541
MET272
4.012
ARG274
2.725
SER275
3.517
Residue
Distance (Å)
SER278
4.210
TRP286
3.507
CYS288
4.067
VAL300
3.773
ALA303
4.992
HIS305
2.673
LEU309
3.774
LEU313
4.113
GLN317
4.848
TYR395
3.676
TYR401
3.815
LEU404
3.948
LEU414
3.750
VAL418
4.089
PHE422
3.622
HIS497
2.732
Ligand Name: {4-[3-(4-{[(2r)-2-Hydroxy-3,3-Dimethylbutyl]oxy}-3-Methylphenyl)pentan-3-Yl]-2-Methylphenoxy}acetic Acid Ligand Info
Structure Description Crystal Structure Analysis of Vitamin D receptor PDB:3AZ1
Method X-ray diffraction Resolution 1.50 Å Mutation No [24]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPLLYAKM
383
IQKLADLRSL
393
NEEHSKQYRC
403
LSFQPECSMK
413
LTPLVLEVFG
423
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DS2 or .DS22 or .DS23 or :3DS2;style chemicals stick;color identity;select .A:143 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:237 or .A:271 or .A:272 or .A:274 or .A:275 or .A:277 or .A:278 or .A:286 or .A:288 or .A:295 or .A:296 or .A:300 or .A:305 or .A:309 or .A:313 or .A:317 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR143
2.604
TYR147
3.642
PHE150
3.804
LEU227
3.995
LEU230
4.039
ALA231
3.532
LEU233
3.491
VAL234
3.707
SER237
3.070
ILE271
3.417
MET272
3.970
ARG274
3.543
SER275
3.027
GLU277
4.849
SER278
2.724
Residue
Distance (Å)
TRP286
3.588
CYS288
3.819
TYR295
3.727
ARG296
4.998
VAL300
3.704
HIS305
2.610
LEU309
3.551
LEU313
4.186
GLN317
4.888
HIS397
2.681
TYR401
3.773
LEU404
3.733
LEU414
3.906
VAL418
4.244
PHE422
3.712
Ligand Name: 5-{4-[3-(4-{[(2r)-2-Hydroxy-3,3-Dimethylbutyl]oxy}-3-Methylphenyl)pentan-3-Yl]-2-Methylphenoxy}pentanoic Acid Ligand Info
Structure Description Crystal Structure Analysis of Vitamin D receptor PDB:3AZ2
Method X-ray diffraction Resolution 1.69 Å Mutation No [24]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPLLYAKM
383
IQKLADLRSL
393
NEEHSKQYRC
403
LSFQPECSMK
413
LTPLVLEVFG
423
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DS3 or .DS32 or .DS33 or :3DS3;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:305 or .A:309 or .A:313 or .A:317 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.449
TYR143
3.164
ASP144
4.571
PHE150
3.785
LEU227
3.900
LEU230
3.982
ALA231
3.564
LEU233
3.769
VAL234
3.602
TYR236
3.457
SER237
2.360
LYS240
3.771
ILE271
3.710
MET272
3.985
ARG274
2.505
SER275
3.473
Residue
Distance (Å)
SER278
3.347
TRP286
3.486
CYS288
3.403
TYR295
3.786
VAL300
3.823
HIS305
2.542
LEU309
3.727
LEU313
4.098
GLN317
4.739
HIS397
2.729
TYR401
3.890
LEU404
3.638
LEU414
3.834
VAL418
4.163
PHE422
3.832
Ligand Name: (4s)-4-Hydroxy-5-[2-Methyl-4-(3-{3-Methyl-4-[4,4,4-Trifluoro-3-Hydroxy-3-(Trifluoromethyl)but-1-Yn-1-Yl]phenyl}pentan-3-Yl)phenoxy]pentanoic Acid Ligand Info
Structure Description Crystal Structure Analysis of Vitamin D receptor PDB:3W0A
Method X-ray diffraction Resolution 1.80 Å Mutation No [25]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPLLYAKM
383
IQKLADLRSL
393
NEEHSKQYRC
403
LSFQPECSMK
413
LTPLVLEVFG
423
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DS5 or .DS52 or .DS53 or :3DS5;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:317 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.597
TYR143
3.492
ASP144
4.815
TYR147
4.735
PHE150
3.855
LEU227
3.119
LEU230
3.921
ALA231
3.561
LEU233
3.595
VAL234
3.382
TYR236
3.978
SER237
3.135
LYS240
3.561
ILE268
3.938
ILE271
3.647
MET272
4.056
ARG274
2.719
Residue
Distance (Å)
SER275
3.569
SER278
4.051
TRP286
3.508
CYS288
4.075
TYR295
3.683
VAL300
3.787
ALA303
4.008
HIS305
2.706
LEU309
3.870
LEU313
4.010
GLN317
4.892
HIS397
2.730
TYR401
3.494
LEU404
3.360
LEU414
3.422
VAL418
3.408
PHE422
3.433
Ligand Name: (4s)-4-Hydroxy-5-[2-Methyl-4-(3-{3-Methyl-4-[(1e)-4,4,4-Trifluoro-3-Hydroxy-3-(Trifluoromethyl)but-1-En-1-Yl]phenyl}pentan-3-Yl)phenoxy]pentanoic Acid Ligand Info
Structure Description Crystal Structure Analysis of Vitamin D receptor PDB:3W0C
Method X-ray diffraction Resolution 1.90 Å Mutation No [26]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPLLYAKM
383
IQKLADLRSL
393
NEEHSKQYRC
403
LSFQPECSMK
413
LTPLVLEVFG
423
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6DS or .6DS2 or .6DS3 or :36DS;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.568
TYR143
3.454
ASP144
4.724
TYR147
4.382
PHE150
3.945
LEU227
3.199
LEU230
3.690
ALA231
3.463
LEU233
3.608
VAL234
3.244
TYR236
3.774
SER237
2.768
LYS240
3.580
ILE268
3.723
ILE271
3.337
MET272
4.239
ARG274
2.758
Residue
Distance (Å)
SER275
3.621
SER278
3.936
TRP286
3.357
CYS288
4.033
TYR295
3.633
VAL300
3.748
ALA303
3.967
HIS305
2.702
LEU309
3.777
LEU313
4.021
HIS397
2.692
TYR401
3.383
LEU404
3.415
LEU414
3.534
VAL418
3.429
PHE422
3.435
Ligand Name: [3-Fluoro-2'-Methyl-4'-(3-{3-Methyl-4-[(1e)-4,4,4-Trifluoro-3-Hydroxy-3-(Trifluoromethyl)but-1-En-1-Yl]phenyl}pentan-3-Yl)biphenyl-4-Yl]acetic Acid Ligand Info
Structure Description Crystal Structure Analysis of Vitamin D receptor PDB:3W0Y
Method X-ray diffraction Resolution 1.98 Å Mutation No [27]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPLLYAKM
383
IQKLADLRSL
393
NEEHSKQYRC
403
LSFQPECSMK
413
LTPLVLEVFG
423
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DS4 or .DS42 or .DS43 or :3DS4;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:153 or .A:227 or .A:230 or .A:231 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:317 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
4.391
TYR143
3.311
ASP144
2.778
TYR147
4.036
PHE150
3.408
PHE153
4.808
LEU227
3.201
LEU230
3.701
ALA231
3.215
LEU233
3.888
VAL234
3.400
TYR236
3.038
SER237
3.475
LYS240
4.910
ILE268
3.492
ILE271
3.756
MET272
4.010
ARG274
2.736
Residue
Distance (Å)
SER275
3.388
SER278
3.722
TRP286
3.613
CYS288
3.494
TYR295
3.863
VAL300
3.916
ALA303
3.945
HIS305
2.733
LEU309
3.947
LEU313
4.144
GLN317
4.703
HIS397
2.751
TYR401
3.243
LEU404
3.314
LEU414
3.472
VAL418
3.427
PHE422
3.538
Ligand Name: Eldecalcitol Ligand Info
Structure Description Crystal Structure Analysis of Vitamin D receptor PDB:3WGP
Method X-ray diffraction Resolution 2.00 Å Mutation No [28]
PDB Sequence
LRPKLSEEQQ
129
RIIAILLDAH
139
HKTYDPTYSD
149
FCQFRPPVRV
159
NDGGGSVTLE
220

LSQLSMLPHL
230
ADLVSYSIQK
240
VIGFAKMIPG
250
FRDLTSEDQI
260
VLLKSSAIEV
270

IMLRSNESFT
280
MDDMSWTCGN
290
QDYKYRVSDV
300
TKAGHSLELI
310
EPLIKFQVGL
320

KKLNLHEEEH
330
VLLMAICIVS
340
PDRPGVQDAA
350
LIEAIQDRLS
360
NTLQTYIRCR
370

HPPPLLYAKM
383
IQKLADLRSL
393
NEEHSKQYRC
403
LSFQPECSMK
413
LTPLVLEVFG
423
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ED9 or .ED92 or .ED93 or :3ED9;style chemicals stick;color identity;select .A:142 or .A:143 or .A:144 or .A:147 or .A:150 or .A:227 or .A:230 or .A:233 or .A:234 or .A:236 or .A:237 or .A:240 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:286 or .A:288 or .A:295 or .A:300 or .A:303 or .A:305 or .A:309 or .A:313 or .A:397 or .A:401 or .A:404 or .A:414 or .A:418 or .A:422; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR142
3.183
TYR143
2.785
ASP144
3.774
TYR147
3.929
PHE150
4.179
LEU227
3.407
LEU230
3.955
LEU233
3.798
VAL234
3.435
TYR236
3.551
SER237
2.785
LYS240
3.254
ILE268
4.132
ILE271
3.651
MET272
4.091
ARG274
2.802
Residue
Distance (Å)
SER275
3.337
SER278
2.721
TRP286
3.370
CYS288
3.488
TYR295
3.989
VAL300
3.642
ALA303
4.704
HIS305
2.778
LEU309
3.574
LEU313
3.840
HIS397
2.760
TYR401
3.931
LEU404
4.082
LEU414
4.399
VAL418
3.870
PHE422
4.501
References  Top
REF 1 Crystal structures of the vitamin D nuclear receptor liganded with the vitamin D side chain analogues calcipotriol and seocalcitol, receptor agonists of clinical importance. Insights into a structural basis for the switching of calcipotriol to a receptor antagonist by further side chain modification. J Med Chem. 2004 Apr 8;47(8):1956-61.
REF 2 Crystal structures of the vitamin D receptor complexed to superagonist 20-epi ligands. Proc Natl Acad Sci U S A. 2001 May 8;98(10):5491-6.
REF 3 Human VDR ligand binding domain in complex with maxacalcitol
REF 4 Superagonistic action of 14-epi-analogs of 1,25-dihydroxyvitamin D explained by vitamin D receptor-coactivator interaction. Mol Pharmacol. 2005 May;67(5):1566-73.
REF 5 Synthesis, structure, and biological activity of des-side chain analogues of 1Alpha,25-dihydroxyvitamin?D3 with substituents at C18. ChemMedChem. 2011 May 2;6(5):788-93.
REF 6 Structure-function relationships and crystal structures of the vitamin D receptor bound 2 alpha-methyl-(20S,23S)- and 2 alpha-methyl-(20S,23R)-epoxymethano-1 alpha,25-dihydroxyvitamin D3. J Med Chem. 2010 Feb 11;53(3):1159-71.
REF 7 Structure-based design of a superagonist ligand for the vitamin D nuclear receptor. Chem Biol. 2008 Apr;15(4):383-92.
REF 8 Probing a water channel near the A-ring of receptor-bound 1 alpha,25-dihydroxyvitamin D3 with selected 2 alpha-substituted analogues. J Med Chem. 2006 Aug 24;49(17):5199-205.
REF 9 Structural basis of the activation of the human Vitamin D receptor by the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3
REF 10 Revisiting the 7,8-cis-vitamin D3 derivatives: synthesis, evaluating the biological activity, and study of the binding configuration
REF 11 Revisiting the 7,8-cis-vitamin D3 derivatives: synthesis, evaluating the biological activity, and study of the binding configuration
REF 12 Development of 14-epi-19-nortachysterol and its unprecedented binding configuration for the human vitamin D receptor. J Am Chem Soc. 2011 May 11;133(18):7215-21.
REF 13 Synthesis of novel C-2 substituted vitamin D derivatives having ringed side chains and their biological evaluation on bone. J Steroid Biochem Mol Biol. 2013 Jul;136:3-8.
REF 14 Synthesis of 2Alpha-heteroarylalkyl active vitamin d3 with therapeutic effect on enhancing bone mineral density in vivo. ACS Med Chem Lett. 2013 May 28;4(7):671-4.
REF 15 New C15-substituted active vitamin D3. Org Lett. 2011 Jun 3;13(11):2852-5.
REF 16 Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D3-26,23-lactone. Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):918-26.
REF 17 Synthesis and biological activities of vitamin D3 derivatives with cyanoalkyl side chain at C-2 position. J Steroid Biochem Mol Biol. 2015 Apr;148:27-30.
REF 18 Design, Chemical synthesis, Functional characterization and Crystal structure of the sidechain analogue of 1,25-dihydroxyvitamin D3.
REF 19 Structural basis for the accommodation of bis- and tris-aromatic derivatives in vitamin D nuclear receptor. J Med Chem. 2012 Oct 11;55(19):8440-9.
REF 20 Crystal structure of a vitamin D3 analog, ZK203278, showing dissociated profile. Anticancer Res. 2012 Jan;32(1):335-9.
REF 21 HDX reveals the conformational dynamics of DNA sequence specific VDR co-activator interactions. Nat Commun. 2017 Oct 13;8(1):923.
REF 22 Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol
REF 23 Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor. Org Biomol Chem. 2018 Apr 4;16(14):2448-2455.
REF 24 Novel nonsecosteroidal vitamin D3 carboxylic acid analogs for osteoporosis, and SAR analysis. Bioorg Med Chem. 2011 Aug 15;19(16):4721-9.
REF 25 structure analysis of vitamin D3 receptor
REF 26 structure analysis of vitamin D receptor
REF 27 Crystal Structure Analysis of Vitamin D receptor
REF 28 Crystal Structure Analysis of Vitamin D receptor

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