Target Binding Site Detail
| 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 | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Calcitriol | Ligand Info | |||
| Canonical SMILES | CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(CC(C3=C)O)O)C | ||||
| InChI | 1S/C27H44O3/c1-18(8-6-14-26(3,4)30)23-12-13-24-20(9-7-15-27(23,24)5)10-11-21-16-22(28)17-25(29)19(21)2/h10-11,18,22-25,28-30H,2,6-9,12-17H2,1,3-5H3/b20-10+,21-11-/t18-,22-,23-,24+,25+,27-/m1/s1 | ||||
| InChIKey | GMRQFYUYWCNGIN-NKMMMXOESA-N | ||||
| PubChem Compound ID | 5280453 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1IE9 Crystal Structure Of The Nuclear Receptor For Vitamin D Ligand Binding Domain Bound to MC1288 | ||||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | No | [1] |
| PDB Sequence |
DSLRPKLSEE
127 QQRIIAILLD137 AHHKTYDPTY147 SDFCQFRPPV157 RVNDGGGSVT218 LELSQLSMLP 228 HLADLVSYSI238 QKVIGFAKMI248 PGFRDLTSED258 QIVLLKSSAI268 EVIMLRSNES 278 FTMDDMSWTC288 GNQDYKYRVS298 DVTKAGHSLE308 LIEPLIKFQV318 GLKKLNLHEE 328 EHVLLMAICI338 VSPDRPGVQD348 AALIEAIQDR358 LSNTLQTYIR368 CRHPPPGSHL 378 LYAKMIQKLA388 DLRSLNEEHS398 KQYRCLSFQP408 ECSMKLTPLV418 LEVFG |
|||||
|
|
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
|
|||||
| PDB ID: 1DB1 CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO VITAMIN D | ||||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [2] |
| PDB Sequence |
LRPKLSEEQQ
129 RIIAILLDAH139 HKTYDPTYSD149 FCQFRPPVRV159 NDGGGSVTLE220 LSQLSMLPHL 230 ADLVSYSIQK240 VIGFAKMIPG250 FRDLTSEDQI260 VLLKSSAIEV270 IMLRSNESFT 280 MDDMSWTCGN290 QDYKYRVSDV300 TKAGHSLELI310 EPLIKFQVGL320 KKLNLHEEEH 330 VLLMAICIVS340 PDRPGVQDAA350 LIEAIQDRLS360 NTLQTYIRCR370 HPPPLLYAKM 383 IQKLADLRSL393 NEEHSKQYRC403 LSFQPECSMK413 LTPLVLEVFG423 |
|||||
|
|
TYR143
2.826
TYR147
3.847
PHE150
4.178
LEU227
3.538
LEU230
3.964
LEU233
3.544
VAL234
3.645
SER237
2.781
ILE268
4.280
ILE271
3.894
MET272
4.222
ARG274
2.858
SER275
3.317
SER278
2.914
|
|||||
| PDB ID: 3M7R Crystal structure of VDR H305Q mutant | ||||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | Yes | [3] |
| PDB Sequence |
LRPKLSEEQQ
129 RIIAILLDAH139 HKTYDPTYSD149 FCQFRPPVRV159 NDGGGSVTLE220 LSQLSMLPHL 230 ADLVSYSIQK240 VIGFAKMIPG250 FRDLTSEDQI260 VLLKSSAIEV270 IMLRSNESFT 280 MDDMSWTCGN290 QDYKYRVSDV300 TKAGQSLELI310 EPLIKFQVGL320 KKLNLHEEEH 330 VLLMAICIVS340 PDRPGVQDAA350 LIEAIQDRLS360 NTLQTYIRCR370 HPPPGSHLLY 380 AKMIQKLADL390 RSLNEEHSKQ400 YRCLSFQPEC410 SMKLTPLVLE420 VFG |
|||||
|
|
TYR143
2.784
TYR147
3.757
PHE150
3.991
LEU227
3.599
LEU230
3.853
LEU233
3.527
VAL234
3.446
SER237
2.839
ILE268
4.297
ILE271
3.819
MET272
4.356
ARG274
2.794
SER275
3.294
SER278
2.793
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | 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 2 | The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand. Mol Cell. 2000 Jan;5(1):173-9. | ||||
| REF 3 | Crystal structure of hereditary vitamin D-resistant rickets--associated mutant H305Q of vitamin D nuclear receptor bound to its natural ligand. J Steroid Biochem Mol Biol. 2010 Jul;121(1-2):84-7. | ||||
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