Structure of PDB 5xzf Chain A Binding Site BS02

Receptor Information
>5xzf Chain A (length=237) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRPLSMLPHLADLVSY
SIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW
DCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQK
LADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFG
Ligand information
Ligand ID8J0
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-LLLPRGGASA-N
SMILES
SoftwareSMILES
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=C6/C[C@@H](O)C[C@H](O)C6=C
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
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,6S)-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 chain5xzf Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xzf 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.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y143 L223 V230 S233 R270 S271 S274 W282 Y291 H301 H393
Binding residue
(residue number reindexed from 1)		Y21 L41 V48 S51 R88 S89 S92 W100 Y109 H119 H211
Annotation score1
Binding affinityMOAD: ic50=0.24nM
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:5xzf, PDBe:5xzf, PDBj:5xzf
PDBsum5xzf
PubMed29989817
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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