Structure of PDB 5xpn Chain A Binding Site BS02

Receptor Information
>5xpn 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 ID8BO
InChIInChI=1S/C32H46O4/c1-21(7-5-9-31(36-4)25-12-14-26(33)15-13-25)27-16-17-28-24(8-6-18-32(27,28)3)11-10-23-19-29(34)22(2)30(35)20-23/h10-15,21,27-31,33-35H,2,5-9,16-20H2,1,3-4H3/b24-11+/t21-,27-,28+,29-,30-,31+,32-/m1/s1
InChIKeyLNLTYAYGVNOEBQ-CLQLOTFESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CO[C@@H](CCC[C@@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)C(=C)[C@H](O)C3)c4ccc(O)cc4
CACTVS 3.385CO[CH](CCC[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3)c4ccc(O)cc4
OpenEye OEToolkits 2.0.6CC(CCCC(c1ccc(cc1)O)OC)C2CCC3C2(CCCC3=CC=C4CC(C(=C)C(C4)O)O)C
OpenEye OEToolkits 2.0.6C[C@H](CCC[C@@H](c1ccc(cc1)O)OC)[C@H]2CC[C@@H]\3[C@@]2(CCC/C3=C\C=C4C[C@H](C(=C)[C@@H](C4)O)O)C
FormulaC32 H46 O4
Name(1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{S})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol;
25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3
ChEMBL
DrugBank
ZINC
PDB chain5xpn 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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PDB5xpn 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
Resolution1.96 Å
Binding residue
(original residue number in PDB)		Y143 L223 V230 S233 R270 S271 S274 W282 C284 A299 H301 L400
Binding residue
(residue number reindexed from 1)		Y21 L43 V50 S53 R90 S91 S94 W102 C104 A119 H121 L220
Annotation score1
Binding affinityMOAD: ic50=102nM
PDBbind-CN: -logKd/Ki=6.99,IC50=102nM
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:5xpn, PDBe:5xpn, PDBj:5xpn
PDBsum5xpn
PubMed28954197
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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