Structure of PDB 6b0z Chain B Binding Site BS03

Receptor Information
>6b0z Chain B (length=409) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGHHADQYRATDFVVPGPGKVEI
TYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKG
WPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDM
VAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVE
AEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAF
FANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGEN
LKIKLAQAK
Ligand information
Ligand IDC81
InChIInChI=1S/C23H22F4N6O2/c1-12-8-17(30-10-16(12)15-4-6-28-19(9-15)23(25,26)27)14(3)31-21-29-7-5-20(32-21)33-18(13(2)24)11-35-22(33)34/h4-10,13-14,18H,11H2,1-3H3,(H,29,31,32)/t13-,14-,18+/m0/s1
InChIKeyDCGDPJCUIKLTDU-SUNYJGFJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(ncc1c2ccnc(c2)C(F)(F)F)C(C)Nc3nccc(n3)N4C(COC4=O)C(C)F
CACTVS 3.385C[CH](F)[CH]1COC(=O)N1c2ccnc(N[CH](C)c3cc(C)c(cn3)c4ccnc(c4)C(F)(F)F)n2
ACDLabs 12.01c2(nccc(N1C(OCC1C(F)C)=O)n2)NC(c4ncc(c3ccnc(c3)C(F)(F)F)c(C)c4)C
OpenEye OEToolkits 2.0.6Cc1cc(ncc1c2ccnc(c2)C(F)(F)F)[C@H](C)Nc3nccc(n3)N4[C@H](COC4=O)[C@H](C)F
CACTVS 3.385C[C@H](F)[C@H]1COC(=O)N1c2ccnc(N[C@@H](C)c3cc(C)c(cn3)c4ccnc(c4)C(F)(F)F)n2
FormulaC23 H22 F4 N6 O2
Name(4R)-4-[(1S)-1-fluoroethyl]-3-[2-({(1S)-1-[4-methyl-2'-(trifluoromethyl)[3,4'-bipyridin]-6-yl]ethyl}amino)pyrimidin-4-yl]-1,3-oxazolidin-2-one
ChEMBLCHEMBL3947537
DrugBank
ZINC
PDB chain6b0z Chain D Residue 504 [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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PDB6b0z Discovery and Evaluation of Clinical Candidate IDH305, a Brain Penetrant Mutant IDH1 Inhibitor.
Resolution2.334 Å
Binding residue
(original residue number in PDB)		Q277 V281
Binding residue
(residue number reindexed from 1)		Q273 V277
Annotation score1
Binding affinityMOAD: ic50=0.018uM
BindingDB: IC50=50nM
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:6b0z, PDBe:6b0z, PDBj:6b0z
PDBsum6b0z
PubMed29057061
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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