Structure of PDB 6bl1 Chain B Binding Site BS01

Receptor Information
>6bl1 Chain B (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 IDDWG
InChIInChI=1S/C26H24N4O/c1-17-22-13-12-18-16-28-25(29-21-10-6-3-7-11-21)30-24(18)26(22,14-19(15-27)23(17)31)20-8-4-2-5-9-20/h2-11,16-17,19,22H,12-14H2,1H3,(H,28,29,30)/t17-,19?,22-,26+/m0/s1
InChIKeyZJPWPENZDAACRJ-BXZAVOJSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@H]1[C@@H]2CCc3cnc(nc3[C@]2(CC(C1=O)C#N)c4ccccc4)Nc5ccccc5
OpenEye OEToolkits 2.0.6CC1C2CCc3cnc(nc3C2(CC(C1=O)C#N)c4ccccc4)Nc5ccccc5
CACTVS 3.385C[C@H]1[C@@H]2CCc3cnc(Nc4ccccc4)nc3[C@]2(C[C@@H](C#N)C1=O)c5ccccc5
CACTVS 3.385C[CH]1[CH]2CCc3cnc(Nc4ccccc4)nc3[C]2(C[CH](C#N)C1=O)c5ccccc5
ACDLabs 12.01C4(=O)C(C#N)CC5(c1ccccc1)c3c(cnc(Nc2ccccc2)n3)CCC5C4C
FormulaC26 H24 N4 O
Name(6aS,7S,9S,10aS)-7-methyl-8-oxo-10a-phenyl-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile
ChEMBLCHEMBL4551778
DrugBank
ZINC
PDB chain6bl1 Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6bl1 Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of His315.
Resolution2.02 Å
Binding residue
(original residue number in PDB)		H309 V312 R314 H315 M318 T325 N328 K374 L383
Binding residue
(residue number reindexed from 1)		H307 V310 R312 H313 M316 T323 N326 K372 L381
Annotation score1
Binding affinityMOAD: ic50=110nM
PDBbind-CN: -logKd/Ki=6.96,IC50=110nM
BindingDB: IC50=1770nM
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bl1, PDBe:6bl1, PDBj:6bl1
PDBsum6bl1
PubMed30004704
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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