Structure of PDB 5gic Chain A Binding Site BS02

Receptor Information
>5gic Chain A (length=237) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRPLSMLPHLADLVSYS
IQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWD
CGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAIC
IVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKL
ADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN
Ligand information
Ligand IDDLC
InChIInChI=1S/C35H49NO4/c1-23(19-28-22-35(4,40)33(39)36(28)18-16-25-9-6-5-7-10-25)30-14-15-31-26(11-8-17-34(30,31)3)12-13-27-20-29(37)21-32(38)24(27)2/h5-7,9-10,12-13,23,28-32,37-38,40H,2,8,11,14-22H2,1,3-4H3/b26-12-,27-13+/t23-,28+,29-,30-,31+,32+,34-,35-/m1/s1
InChIKeyKMTLDHCLGFVLKS-YMDIQGDRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(CC1CC(C(=O)N1CCc2ccccc2)(C)O)C3CCC4C3(CCCC4=CC=C5CC(CC(C5=C)O)O)C
OpenEye OEToolkits 2.0.7C[C@H](C[C@H]1C[C@@](C(=O)N1CCc2ccccc2)(C)O)[C@H]3CC[C@@H]\4[C@@]3(CCC/C4=C/C=C/5\C[C@H](C[C@@H](C5=C)O)O)C
CACTVS 3.385C[CH](C[CH]1C[C](C)(O)C(=O)N1CCc2ccccc2)[CH]3CC[CH]4C(CCC[C]34C)=CC=C5C[CH](O)C[CH](O)C5=C
CACTVS 3.385C[C@H](C[C@H]1C[C@@](C)(O)C(=O)N1CCc2ccccc2)[C@H]3CC[C@H]4\C(CCC[C@]34C)=C/C=C/5C[C@@H](O)C[C@H](O)C/5=C
FormulaC35 H49 N O4
Name(3~{R},5~{S})-5-[(2~{R})-2-[(1~{R},3~{a}~{S},4~{Z},7~{a}~{R})-7~{a}-methyl-4-[(2~{E})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(2-phenylethyl)pyrrolidin-2-one
ChEMBL
DrugBank
ZINC
PDB chain5gic Chain A Residue 501 [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]
PDB5gic Regulation of the vitamin D receptor by vitamin D lactam derivatives.
Resolution2.352 Å
Binding residue
(original residue number in PDB)
S233 I267 R270 S271 S274 W282 V296 H393 Y397
Binding residue
(residue number reindexed from 1)
S50 I84 R87 S88 S91 W99 V113 H210 Y214
Annotation score1
Binding affinityMOAD: Kd=330.9nM
PDBbind-CN: -logKd/Ki=6.48,Kd=330.9nM
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

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:5gic, PDBe:5gic, PDBj:5gic
PDBsum5gic
PubMed27500498
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

[Back to BioLiP]