Structure of PDB 8pz7 Chain A Binding Site BS02

Receptor Information
>8pz7 Chain A (length=237) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVRRLSMLPHLADLVSY
SIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSW
SCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAI
CLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLA
DLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSE
Ligand information
Ligand IDIG0
InChIInChI=1S/C29H50O3/c1-20(10-8-16-28(3,4)32)24-12-6-7-13-25-23(11-9-17-29(24,25)5)15-14-22-18-26(30)21(2)27(31)19-22/h14-15,20-21,24-27,30-32H,6-13,16-19H2,1-5H3/b22-14-,23-15+/t20-,21-,24+,25+,26-,27-,29-/m1/s1
InChIKeyAVNUSPMNPZNONM-DHXJDUGVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1[C@@H](CC(=C/C=C/2\CCC[C@]3([C@H]2CCCC[C@H]3[C@H](C)CCCC(C)(C)O)C)C[C@H]1O)O
CACTVS 3.385C[C@H](CCCC(C)(C)O)[C@@H]1CCCC[C@H]2C(/CCC[C@]12C)=C/[CH]=[C@]3C[C@@H](O)[CH](C)[C@H](O)C3
CACTVS 3.385C[CH](CCCC(C)(C)O)[CH]1CCCC[CH]2C(CCC[C]12C)=C[CH]=[C]3C[CH](O)[CH](C)[CH](O)C3
OpenEye OEToolkits 2.0.7CC1C(CC(=CC=C2CCCC3(C2CCCCC3C(C)CCCC(C)(C)O)C)CC1O)O
FormulaC29 H50 O3
Name(1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{R},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,8,9,9~{a}-hexahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]-2-methyl-cyclohexane-1,3-diol
ChEMBL
DrugBank
ZINC
PDB chain8pz7 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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PDB8pz7 Design, Synthesis, Biological Activity of D-Bishomo-1a,25-dihydroxyvitamin D3 Analogs and their Crystal Structures with the Vitamin D Nuclear Receptor
Resolution2.93 Å
Binding residue
(original residue number in PDB)		Y175 S265 R302 S303 S306 W314 C316 V328 H333 H423
Binding residue
(residue number reindexed from 1)		Y21 S51 R88 S89 S92 W100 C102 V114 H119 H209
Annotation score1
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:8pz7, PDBe:8pz7, PDBj:8pz7
PDBsum8pz7
PubMed38615411
UniProtQ9PTN2|VDRA_DANRE Vitamin D3 receptor A (Gene Name=vdra)

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