Structure of PDB 3vjs Chain A Binding Site BS02

Receptor Information
>3vjs Chain A (length=239) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRPLSMLPHLADLVSY
SIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW
DCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQK
LADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNE
Ligand information
Ligand ID10S
InChIInChI=1S/C17H42B10O4/c1-3-15(30,4-2)8-5-6-9-16-18-19(16)21(16)22(16)20(16,18)24(18)17(10-12-31-13-14(29)7-11-28)23(18,19,24)25(17,19,21)27(17,21,22)26(17,20,22)24/h14,18-30H,3-13H2,1-2H3/t14-/m0/s1
InChIKeyCZLKNINFVMBXBM-AWEZNQCLSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCC(O)(CC)CCCC[C]1234[BH]567[BH]189[BH]2%10%11[BH]3%12%13[BH]45%14[BH]6%15%16[BH]78%17[BH]9%10%18[BH]%11%12%19[BH]%13%14%15[C]%16%17%18%19CCOC[C@@H](O)CCO
OpenEye OEToolkits 1.7.6[BH]1234[BH]567[BH]189[BH]212[BH]33%10C454([BH]656[BH]433[BH]%1011[BH]353[BH]768C9213CCOCC(CCO)O)CCCCC(CC)(CC)O
CACTVS 3.370CCC(O)(CC)CCCC[C]1234[BH]567[BH]189[BH]2%10%11[BH]3%12%13[BH]45%14[BH]6%15%16[BH]78%17[BH]9%10%18[BH]%11%12%19[BH]%13%14%15[C]%16%17%18%19CCOC[CH](O)CCO
OpenEye OEToolkits 1.7.6[BH]1234[BH]567[BH]189[BH]212[BH]33%10C454([BH]656[BH]433[BH]%1011[BH]353[BH]768C9213CCOC[C@H](CCO)O)CCCCC(CC)(CC)O
FormulaC17 H42 B10 O4
Name1-(2-[(S)-2,4-Dihydroxybutoxy]ethyl)-12-(5-ethyl-5-hydroxyheptyl)-1,12-dicarba-closo-dodecaborane
ChEMBL
DrugBank
ZINC
PDB chain3vjs 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]
PDB3vjs Boron Cluster-based Development of Potent Nonsecosteroidal Vitamin D Receptor Ligands: Direct Observation of Hydrophobic Interaction between Protein Surface and Carborane
Resolution1.93 Å
Binding residue
(original residue number in PDB)
V230 S233 I267 R270 S271 S274 W282 V296 H301 H393
Binding residue
(residue number reindexed from 1)
V48 S51 I85 R88 S89 S92 W100 V114 H119 H211
Annotation score1
Binding affinityMOAD: ic50=0.64uM
PDBbind-CN: -logKd/Ki=6.19,IC50=0.64uM
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:3vjs, PDBe:3vjs, PDBj:3vjs
PDBsum3vjs
PubMed22066785
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

[Back to BioLiP]