Structure of PDB 4rup Chain A Binding Site BS02

Receptor Information
>4rup 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
WSCGGPDFKYCINDVTKAGHTLEHLEPLVKFQVGLKKLKLHEEEHVLLMA
ICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKL
ADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEV
Ligand information
Ligand IDH97
InChIInChI=1S/C31H44F6O4/c1-27(2,40)14-4-7-21(9-6-16-29(41,30(32,33)34)31(35,36)37)25-12-13-26-22(8-5-15-28(25,26)3)11-10-20-17-23(38)19-24(39)18-20/h10-11,21,23-26,38-41H,4-5,7-9,12-15,17-19H2,1-3H3/b22-11+/t21-,23-,24-,25-,26+,28-/m1/s1
InChIKeyRAYDHJNMFBHXHA-DUSBBPLISA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC(F)(F)C(O)(C#CCC(CCCC(O)(C)C)C2CCC3C(=C\C=C1\CC(O)CC(O)C1)\CCCC23C)C(F)(F)F
CACTVS 3.370CC(C)(O)CCC[CH](CC#CC(O)(C(F)(F)F)C(F)(F)F)[CH]1CC[CH]2C(CCC[C]12C)=C[CH]=[C]3C[CH](O)[CH2][CH](O)C3
CACTVS 3.370CC(C)(O)CCC[C@H](CC#CC(O)(C(F)(F)F)C(F)(F)F)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/[CH]=[C]3C[C@@H](O)[CH2][C@H](O)C3
OpenEye OEToolkits 1.7.0CC12CCCC(=CC=C3CC(CC(C3)O)O)C1CCC2C(CCCC(C)(C)O)CC#CC(C(F)(F)F)(C(F)(F)F)O
OpenEye OEToolkits 1.7.0C[C@]12CCC/C(=C\C=C3C[C@H](C[C@@H](C3)O)O)/[C@@H]1CC[C@@H]2[C@H](CCCC(C)(C)O)CC#CC(C(F)(F)F)(C(F)(F)F)O
FormulaC31 H44 F6 O4
Name(1R,3R,7E,17beta)-17-[(1R)-6,6,6-trifluoro-5-hydroxy-1-(4-hydroxy-4-methylpentyl)-5-(trifluoromethyl)hex-3-yn-1-yl]-9,1 0-secoestra-5,7-diene-1,3-diol;
1,25-dihydroxy-20R-21(3-trideuteromethyl-3-hydroxy-4,4,4-trideuterobutyl)-23-yne-26,27-hexafluoro-19-nor-cholecalcifero l (Gemini--0097)
ChEMBLCHEMBL1738811
DrugBank
ZINCZINC000066156873
PDB chain4rup 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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PDB4rup A vitamin D receptor selectively activated by gemini analogs reveals ligand dependent and independent effects.
Resolution2.75 Å
Binding residue
(original residue number in PDB)
L255 V262 S265 M300 R302 S303 S306 W314 C316 H333 H337 L338 H423 Y427 L430
Binding residue
(residue number reindexed from 1)
L42 V49 S52 M87 R89 S90 S93 W101 C103 H120 H124 L125 H210 Y214 L217
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:4rup, PDBe:4rup, PDBj:4rup
PDBsum4rup
PubMed25620699
UniProtQ9PTN2|VDRA_DANRE Vitamin D3 receptor A (Gene Name=vdra)

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