Structure of PDB 6fo7 Chain A Binding Site BS02

Receptor Information
>6fo7 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 IDLX3
InChIInChI=1S/C28H42O3/c1-5-6-13-23(15-16-24-19-26(29)20-27(30)21(24)2)25-14-10-12-22(18-25)11-8-7-9-17-28(3,4)31/h10,12,14-16,18,26-27,29-31H,2,5-9,11,13,17,19-20H2,1,3-4H3/b23-15+,24-16-/t26-,27+/m1/s1
InChIKeyUWAWDTCFOCGFNY-NTWKYLMFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCC(=CC=C1CC(CC(C1=C)O)O)c2cccc(c2)CCCCCC(C)(C)O
CACTVS 3.385CCCC\C(=C/C=C\1C[C@@H](O)C[C@H](O)C\1=C)c2cccc(CCCCCC(C)(C)O)c2
OpenEye OEToolkits 2.0.6CCCC/C(=C\C=C/1\C[C@H](C[C@@H](C1=C)O)O)/c2cccc(c2)CCCCCC(C)(C)O
CACTVS 3.385CCCCC(=CC=C1C[CH](O)C[CH](O)C1=C)c2cccc(CCCCCC(C)(C)O)c2
FormulaC28 H42 O3
Name(1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]hept-2-enylidene]cyclohexane-1,3-diol
ChEMBLCHEMBL4203464
DrugBank
ZINC
PDB chain6fo7 Chain A Residue 4000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6fo7 Aromatic-Based Design of Highly Active and Noncalcemic Vitamin D Receptor Agonists.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		Y175 L258 S265 I299 R302 S303 S306 W314 C316 Y323 V328 H333 H423
Binding residue
(residue number reindexed from 1)		Y22 L45 S52 I86 R89 S90 S93 W101 C103 Y110 V115 H120 H210
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.87,IC50=13.6nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6fo7, PDBe:6fo7, PDBj:6fo7
PDBsum6fo7
PubMed29733645
UniProtQ9PTN2|VDRA_DANRE Vitamin D3 receptor A (Gene Name=vdra)

[Back to BioLiP]