Structure of PDB 5xpo Chain A Binding Site BS02

Receptor Information
>5xpo 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]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSMLPHLADLV
SYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDM
SWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLM
AICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMI
QKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFG
Ligand information
Ligand ID8BL
InChIInChI=1S/C31H42O4/c1-20(6-4-8-28(33)24-11-13-25(32)14-12-24)26-15-16-27-23(7-5-17-31(26,27)3)10-9-22-18-29(34)21(2)30(35)19-22/h9-14,20,26-27,29-30,32,34-35H,2,4-8,15-19H2,1,3H3/b23-10+/t20-,26-,27+,29-,30-,31-/m1/s1
InChIKeyAVOJSQKILRAHNA-SLEIQBAPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](CCCC(=O)c1ccc(O)cc1)[CH]2CC[CH]3C(CCC[C]23C)=CC=C4C[CH](O)C(=C)[CH](O)C4
OpenEye OEToolkits 2.0.6CC(CCCC(=O)c1ccc(cc1)O)C2CCC3C2(CCCC3=CC=C4CC(C(=C)C(C4)O)O)C
OpenEye OEToolkits 2.0.6C[C@H](CCCC(=O)c1ccc(cc1)O)[C@H]2CC[C@@H]\3[C@@]2(CCC/C3=C\C=C4C[C@H](C(=C)[C@@H](C4)O)O)C
CACTVS 3.385C[C@H](CCCC(=O)c1ccc(O)cc1)[C@H]2CC[C@H]3C(/CCC[C@]23C)=C/C=C/4C[C@@H](O)C(=C)[C@H](O)C/4
FormulaC31 H42 O4
Name(5~{R})-5-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexyl idene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-(4-hydroxyphenyl)hexan-1-one;
25-(hydroxyphenyl)-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3
ChEMBLCHEMBL4084385
DrugBank
ZINC
PDB chain5xpo 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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PDB5xpo Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
Resolution2.28 Å
Binding residue
(original residue number in PDB)		Y143 L223 S233 R270 S271 S274 W282 C284 V296 H301 Y397 L400 L410
Binding residue
(residue number reindexed from 1)		Y21 L43 S53 R90 S91 S94 W102 C104 V116 H121 Y217 L220 L230
Annotation score1
Binding affinityMOAD: ic50=84nM
PDBbind-CN: -logKd/Ki=7.08,IC50=84nM
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:5xpo, PDBe:5xpo, PDBj:5xpo
PDBsum5xpo
PubMed28954197
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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