Structure of PDB 6bkz Chain B Binding Site BS01

Receptor Information
>6bkz Chain B (length=412) 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
ENLKIKLAQAKL
Ligand information
Ligand IDDWM
InChIInChI=1S/C28H28FN5O3/c1-17-14-33(28(37)24-7-4-12-30-24)16-23-25(27(36)31-22-6-3-5-20(13-22)18(2)35)32-34(26(17)23)15-19-8-10-21(29)11-9-19/h3-13,17-18,30,35H,14-16H2,1-2H3,(H,31,36)/t17-,18-/m1/s1
InChIKeyIVFDDVKCCBDPQZ-QZTJIDSGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H](O)c1cccc(NC(=O)c2nn(Cc3ccc(F)cc3)c4[C@H](C)CN(Cc24)C(=O)c5[nH]ccc5)c1
OpenEye OEToolkits 2.0.6CC1CN(Cc2c1n(nc2C(=O)Nc3cccc(c3)C(C)O)Cc4ccc(cc4)F)C(=O)c5ccc[nH]5
CACTVS 3.385C[CH](O)c1cccc(NC(=O)c2nn(Cc3ccc(F)cc3)c4[CH](C)CN(Cc24)C(=O)c5[nH]ccc5)c1
OpenEye OEToolkits 2.0.6C[C@@H]1CN(Cc2c1n(nc2C(=O)Nc3cccc(c3)[C@@H](C)O)Cc4ccc(cc4)F)C(=O)c5ccc[nH]5
ACDLabs 12.01n4c(C(Nc1cccc(c1)C(C)O)=O)c3CN(C(c2cccn2)=O)CC(c3n4Cc5ccc(F)cc5)C
FormulaC28 H28 F N5 O3
Name(7R)-1-[(4-fluorophenyl)methyl]-N-{3-[(1R)-1-hydroxyethyl]phenyl}-7-methyl-5-(1H-pyrrole-2-carbonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine-3-carboxamide
ChEMBLCHEMBL4515358
DrugBank
ZINC
PDB chain6bkz Chain A 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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PDB6bkz Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of His315.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		L120 M259
Binding residue
(residue number reindexed from 1)		L118 M257
Annotation score1
Binding affinityMOAD: ic50=120nM
BindingDB: IC50=120nM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bkz, PDBe:6bkz, PDBj:6bkz
PDBsum6bkz
PubMed30004704
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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