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 (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
Canonical SMILES CC1C(CC(=CC1O)C#CC2=CCCC3(C2CCC3C(C)CCCC(C)(C)O)C)O
InChI 1S/C27H42O3/c1-18(8-6-14-26(3,4)30)22-12-13-23-21(9-7-15-27(22,23)5)11-10-20-16-24(28)19(2)25(29)17-20/h9,16,18-19,22-25,28-30H,6-8,12-15,17H2,1-5H3/t18-,19-,22-,23-,24-,25-,27-/m1/s1
InChIKey YCBJWNMIMDLOPD-ADFBMCJESA-N
PubChem Compound ID 53261165
Drug Binding Sites of Target  Top
PDB ID: 3AUR      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
Method X-ray diffraction Resolution 2.21 Å Mutation No [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
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
2.742
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
PDB ID: 3AUQ      Crystal structure of the human vitamin D receptor ligand binding domain complexed with Yne-diene type analog of active 14-epi-2alpha-methyl-19-norvitamin D3
Method X-ray diffraction Resolution 2.64 Å Mutation No [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
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
2.806
TYR147
3.828
PHE150
3.635
LEU227
3.708
LEU230
4.010
LEU233
3.874
VAL234
3.740
TYR236
4.714
SER237
2.703
ILE268
3.882
ILE271
3.902
MET272
3.953
ARG274
2.854
SER275
3.357
ASN276
4.952
GLU277
4.890
Residue
Distance (Å)
SER278
2.747
TRP286
3.545
CYS288
3.704
TYR295
4.131
VAL300
3.777
ALA303
4.963
HIS305
2.799
LEU309
3.846
LEU313
3.916
HIS397
2.820
TYR401
4.118
LEU404
4.384
LEU414
4.412
VAL418
3.878
PHE422
4.636
References  Top
REF 1 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.

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