Target Binding Site Detail

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Target General Information
Ligand 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
Ligand General Information  Top
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
Canonical SMILES CC(CC1CC(=C)C(=O)O1)C2CCC3C2(CCCC3=CC=C4CC(CC(C4=C)O)O)C
InChI 1S/C27H38O4/c1-16(12-22-13-17(2)26(30)31-22)23-9-10-24-19(6-5-11-27(23,24)4)7-8-20-14-21(28)15-25(29)18(20)3/h7-8,16,21-25,28-29H,2-3,5-6,9-15H2,1,4H3/b19-7+,20-8-/t16-,21+,22-,23+,24-,25-,27+/m0/s1
InChIKey SAODSJHDCZTVAT-HPNZEMCUSA-N
PubChem Compound ID 45479714
Drug Binding Sites of Target  Top
PDB ID: 3A2J      Crystal structure of the human vitamin D receptor (H305F/H397F) ligand binding domain complexed with TEI-9647
Method X-ray diffraction Resolution 2.70 Å Mutation Yes [1]
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
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
PDB ID: 3A2I      Crystal structure of the human vitamin D receptor (H305F) ligand binding domain complexed with TEI-9647
Method X-ray diffraction Resolution 3.27 Å Mutation Yes [1]
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
RSLNEEHSKQ
400
YRCLSFQPEC
410
SMKLTPLVLE
420

VFG
Residue
Distance (Å)
TYR143
3.252
TYR147
4.179
PHE150
3.861
LEU227
3.897
LEU230
4.067
ALA231
3.709
LEU233
3.968
VAL234
3.664
SER237
2.745
ILE268
4.388
ILE271
3.690
MET272
3.858
ARG274
2.892
SER275
3.314
Residue
Distance (Å)
SER278
2.763
TRP286
3.609
CYS288
3.728
TYR295
4.261
VAL300
3.618
PHE305
3.285
LEU309
4.392
LEU313
3.940
HIS397
2.960
TYR401
4.464
LEU414
4.919
VAL418
4.864
PHE422
3.873
References  Top
REF 1 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.

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