Structure of PDB 3dr1 Chain A Binding Site BS02

Receptor Information
>3dr1 Chain A (length=240) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVRRLSMLPHLADLV
SYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDM
SWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLM
AICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQK
LADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEV
Ligand information
Ligand IDC5D
InChIInChI=1S/C24H32F6O3/c1-20(2)17(8-6-7-16-13-18(31)15-19(32)14-16)9-12-21(20,3)10-4-5-11-22(33,23(25,26)27)24(28,29)30/h6-8,17-19,31-33H,4,9-10,12-15H2,1-3H3/b8-6+/t17-,18-,19-,21+/m1/s1
InChIKeyPCHUQQNKOFNVDU-OSXMSNBXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1([C@@H](CC[C@]1(C)CCC#CC(C(F)(F)F)(C(F)(F)F)O)\C=C\C=C2C[C@H](C[C@@H](C2)O)O)C
CACTVS 3.341CC1(C)[C@@H](CC[C@]1(C)CCC#CC(O)(C(F)(F)F)C(F)(F)F)/C=C/C=C2/C[C@@H](O)C[C@H](O)C2
ACDLabs 10.04FC(F)(F)C(O)(C#CCCC2(C)CCC(/C=C/C=C1\CC(O)CC(O)C1)C2(C)C)C(F)(F)F
OpenEye OEToolkits 1.5.0CC1(C(CCC1(C)CCC#CC(C(F)(F)F)(C(F)(F)F)O)C=CC=C2CC(CC(C2)O)O)C
CACTVS 3.341CC1(C)[CH](CC[C]1(C)CCC#CC(O)(C(F)(F)F)C(F)(F)F)C=CC=C2C[CH](O)C[CH](O)C2
FormulaC24 H32 F6 O3
Name(1R,3R)-5-[(2E)-3-{(1S,3R)-2,2,3-trimethyl-3-[6,6,6-trifluoro-5-hydroxy-5-(trifluoromethyl)hex-3-yn-1-yl]cyclopentyl}prop-2-en-1-ylidene]cyclohexane-1,3-diol
ChEMBL
DrugBankDB07530
ZINCZINC000038911928
PDB chain3dr1 Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dr1 Superagonistic fluorinated vitamin D3 analogs stabilize helix 12 of the vitamin D receptor.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Y175 L255 L261 V262 S265 R302 S303 S306 W314 H333 H423 Y427 L430
Binding residue
(residue number reindexed from 1)		Y23 L43 L49 V50 S53 R90 S91 S94 W102 H121 H211 Y215 L218
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:3dr1, PDBe:3dr1, PDBj:3dr1
PDBsum3dr1
PubMed18940664
UniProtQ9PTN2|VDRA_DANRE Vitamin D3 receptor A (Gene Name=vdra)

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