Structure of PDB 6bky Chain E Binding Site BS02

Receptor Information
>6bky Chain E (length=416) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKV
EITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALS
KGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLID
DMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKT
VEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKEL
AFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLG
ENLKIKLAQAKLSLEH
Ligand information
Ligand IDK32
InChIInChI=1S/C7H2Br4N2O/c8-1-2(9)4(11)6-5(3(1)10)12-7(14)13-6/h(H2,12,13,14)
InChIKeyBMVNFJCUHHTZQU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Brc1c2c(c(Br)c(Br)c1Br)NC(=O)N2
CACTVS 3.341Brc1c(Br)c(Br)c2NC(=O)Nc2c1Br
OpenEye OEToolkits 1.5.0c12c(c(c(c(c1Br)Br)Br)Br)NC(=O)N2
FormulaC7 H2 Br4 N2 O
Name4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-ONE
ChEMBLCHEMBL221360
DrugBank
ZINCZINC000013585914
PDB chain6bky Chain E 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]
PDB6bky Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of His315.
Resolution2.17 Å
Binding residue
(original residue number in PDB)		W124 V255 M259 Q277 S280
Binding residue
(residue number reindexed from 1)		W122 V253 M257 Q275 S278
Annotation score1
Binding affinityMOAD: ic50=270nM
BindingDB: IC50=270nM
Enzymatic activity
Enzyme Commision number 1.1.1.42: isocitrate dehydrogenase (NADP(+)).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004450 isocitrate dehydrogenase (NADP+) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0045296 cadherin binding
GO:0046872 metal ion binding
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle
GO:0006102 isocitrate metabolic process
GO:0006103 2-oxoglutarate metabolic process
GO:0006739 NADP metabolic process
GO:0006749 glutathione metabolic process
GO:0006979 response to oxidative stress
GO:0008585 female gonad development
GO:0014070 response to organic cyclic compound
GO:0048545 response to steroid hormone
GO:0060696 regulation of phospholipid catabolic process
GO:0071071 regulation of phospholipid biosynthetic process
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005829 cytosol
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904724 tertiary granule lumen
GO:1904813 ficolin-1-rich granule lumen

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bky, PDBe:6bky, PDBj:6bky
PDBsum6bky
PubMed30004704
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

[Back to BioLiP]