Structure of PDB 6fod Chain A Binding Site BS02

Receptor Information
>6fod Chain A (length=239) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVRRLSMLPHLADLVS
YSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMS
WSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMA
ICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKL
ADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEV
Ligand information
Ligand IDE05
InChIInChI=1S/C26H38O3/c1-5-21(13-14-22-17-24(27)18-25(28)19(22)2)23-12-9-11-20(16-23)10-7-6-8-15-26(3,4)29/h9,11-14,16,24-25,27-29H,2,5-8,10,15,17-18H2,1,3-4H3/b21-13+,22-14-/t24-,25+/m1/s1
InChIKeyBQVXPWDQMUNMLU-FIKMVKLPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC/C(=C\C=C/1\C[C@H](C[C@@H](C1=C)O)O)/c2cccc(c2)CCCCCC(C)(C)O
OpenEye OEToolkits 2.0.6CCC(=CC=C1CC(CC(C1=C)O)O)c2cccc(c2)CCCCCC(C)(C)O
CACTVS 3.385CCC(=CC=C1C[CH](O)C[CH](O)C1=C)c2cccc(CCCCCC(C)(C)O)c2
CACTVS 3.385CC\C(=C/C=C\1C[C@@H](O)C[C@H](O)C\1=C)c2cccc(CCCCCC(C)(C)O)c2
FormulaC26 H38 O3
Name(1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]pent-2-enylidene]cyclohexane-1,3-diol
ChEMBLCHEMBL4202828
DrugBank
ZINC
PDB chain6fod Chain A Residue 4000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fod Aromatic-Based Design of Highly Active and Noncalcemic Vitamin D Receptor Agonists.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y175 S265 I299 R302 S303 S306 W314 C316 Y323 H333 H423 Y427 F448
Binding residue
(residue number reindexed from 1)		Y22 S52 I86 R89 S90 S93 W101 C103 Y110 H120 H210 Y214 F235
Annotation score1
Binding affinityMOAD: ic50=7.11nM
PDBbind-CN: -logKd/Ki=8.15,IC50=7.11nM
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
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6fod, PDBe:6fod, PDBj:6fod
PDBsum6fod
PubMed29733645
UniProtQ9PTN2|VDRA_DANRE Vitamin D3 receptor A (Gene Name=vdra)

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