Structure of PDB 5xzh Chain A Binding Site BS02

Receptor Information
>5xzh Chain A (length=239) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRPLSMLPHLADLV
SYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDM
SWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLM
AICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMI
QKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFG
Ligand information
Ligand ID8J3
InChIInChI=1S/C35H50O3/c1-22(6-4-8-33(38)35-19-24-14-25(20-35)16-26(15-24)21-35)30-11-12-31-27(7-5-13-34(30,31)3)9-10-28-17-29(36)18-32(37)23(28)2/h9-10,22,24-26,29-33,36-38H,2,5-7,11-21H2,1,3H3/b27-9+,28-10-/t22-,24-,25+,26-,29-,30-,31+,32+,33+,34-,35-/m1/s1
InChIKeyRKVGVUCXMUXZTG-JQIDRQNQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@H](CC#C[C@@H](C12CC3CC(C1)CC(C3)C2)O)[C@H]4CC[C@@H]\5[C@@]4(CCC/C5=C\C=C/6\C[C@H](C[C@@H](C6=C)O)O)C
CACTVS 3.385C[C@H](CC#C[C@H](O)C12CC3CC(CC(C3)C1)C2)[C@H]4CC[C@H]5C(\CCC[C@]45C)=C\C=C/6C[C@@H](O)C[C@H](O)C/6=C
OpenEye OEToolkits 2.0.6CC(CC#CC(C12CC3CC(C1)CC(C3)C2)O)C4CCC5C4(CCCC5=CC=C6CC(CC(C6=C)O)O)C
CACTVS 3.385C[CH](CC#C[CH](O)C12CC3CC(CC(C3)C1)C2)[CH]4CC[CH]5C(CCC[C]45C)=CC=C6C[CH](O)C[CH](O)C6=C
FormulaC35 H50 O3
Name(1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,6R)-6-(1-adamantyl)-6-oxidanyl-hex-4-yn-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
ChEMBL
DrugBank
ZINC
PDB chain5xzh Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5xzh 25 S-Adamantyl-23-yne-26,27-dinor-1 alpha ,25-dihydroxyvitamin D3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Y143 L223 V230 S233 R270 S271 S274 W282 C284 H301 H393
Binding residue
(residue number reindexed from 1)		Y23 L43 V50 S53 R90 S91 S94 W102 C104 H121 H213
Annotation score1
Binding affinityMOAD: ic50=3.13nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004879 nuclear receptor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription

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Molecular Function
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Biological Process
External links
PDB RCSB:5xzh, PDBe:5xzh, PDBj:5xzh
PDBsum5xzh
PubMed29989817
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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