Structure of PDB 5tqh Chain D Binding Site BS01

Receptor Information
>5tqh Chain D (length=402) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATN
DQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNIL
GGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVE
ITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSK
GWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDD
MVAQAMKSEGGFIWACKSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHG
TVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALE
EVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLA
QA
Ligand information
Ligand ID7J2
InChIInChI=1S/C23H25FN6O2/c1-13(2)19-12-32-23(31)30(19)20-7-8-25-22(29-20)28-15(4)21-26-10-17(11-27-21)16-5-6-18(24)14(3)9-16/h5-11,13,15,19H,12H2,1-4H3,(H,25,28,29)/t15-,19+/m0/s1
InChIKeyJDCYIMQAIKEACU-HNAYVOBHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(ccc1F)c2cnc(nc2)[C@H](C)Nc3nccc(n3)N4[C@H](COC4=O)C(C)C
ACDLabs 12.01c1(ccc(F)c(C)c1)c2cnc(nc2)C(C)Nc4nccc(N3C(OCC3C(C)C)=O)n4
CACTVS 3.385CC(C)[CH]1COC(=O)N1c2ccnc(N[CH](C)c3ncc(cn3)c4ccc(F)c(C)c4)n2
CACTVS 3.385CC(C)[C@H]1COC(=O)N1c2ccnc(N[C@@H](C)c3ncc(cn3)c4ccc(F)c(C)c4)n2
OpenEye OEToolkits 2.0.6Cc1cc(ccc1F)c2cnc(nc2)C(C)Nc3nccc(n3)N4C(COC4=O)C(C)C
FormulaC23 H25 F N6 O2
Name(4S)-3-[2-({(1S)-1-[5-(4-fluoro-3-methylphenyl)pyrimidin-2-yl]ethyl}amino)pyrimidin-4-yl]-4-(propan-2-yl)-1,3-oxazolidin-2-one
ChEMBLCHEMBL4169151
DrugBank
ZINC
PDB chain5tqh Chain D Residue 501 [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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PDB5tqh Optimization of 3-Pyrimidin-4-yl-oxazolidin-2-ones as Allosteric and Mutant Specific Inhibitors of IDH1.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R109 A111 I113 R119 L120 W124 I128 I130 W267 A282 Y285 M291
Binding residue
(residue number reindexed from 1)		R106 A108 I110 R116 L117 W121 I125 I127 W264 A272 Y275 M281
Annotation score1
Binding affinityMOAD: ic50=0.02uM
BindingDB: IC50=20nM
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
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Cellular Component
External links
PDB RCSB:5tqh, PDBe:5tqh, PDBj:5tqh
PDBsum5tqh
PubMed28197303
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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