Structure of PDB 5svf Chain A Binding Site BS02

Receptor Information
>5svf Chain A (length=398) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATN
DQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNIL
GGTVFREAIICKNIPRLVSGWVKPIIIGHHAATDFVVPGPGKVEITYTPS
DGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYL
STKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAM
KSEGGFIWACKNQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTR
HYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSI
ETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQA
Ligand information
Ligand ID70P
InChIInChI=1S/C18H22N4O2/c1-12(2)15-11-24-18(23)22(15)16-9-10-19-17(21-16)20-13(3)14-7-5-4-6-8-14/h4-10,12-13,15H,11H2,1-3H3,(H,19,20,21)/t13-,15+/m0/s1
InChIKeyCUTPLPKYQGWUBC-DZGCQCFKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)[CH]1COC(=O)N1c2ccnc(N[CH](C)c3ccccc3)n2
OpenEye OEToolkits 2.0.5CC(C)C1COC(=O)N1c2ccnc(n2)NC(C)c3ccccc3
ACDLabs 12.01c1cccc(c1)C(C)Nc2nccc(n2)N3C(COC3=O)C(C)C
OpenEye OEToolkits 2.0.5C[C@@H](c1ccccc1)Nc2nccc(n2)N3[C@H](COC3=O)C(C)C
CACTVS 3.385CC(C)[C@H]1COC(=O)N1c2ccnc(N[C@@H](C)c3ccccc3)n2
FormulaC18 H22 N4 O2
Name(4S)-3-(2-{[(1S)-1-phenylethyl]amino}pyrimidin-4-yl)-4-(propan-2-yl)-1,3-oxazolidin-2-one
ChEMBLCHEMBL3672097
DrugBank
ZINCZINC000142143087
PDB chain5svf 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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PDB5svf Allosteric Mutant IDH1 Inhibitors Reveal Mechanisms for IDH1 Mutant and Isoform Selectivity.
Resolution2.34 Å
Binding residue
(original residue number in PDB)		R109 A111 R119 L120 W124 P127 I128 I130 S278 A282 Y285 M291
Binding residue
(residue number reindexed from 1)		R106 A108 R116 L117 W121 P124 I125 I127 S264 A268 Y271 M277
Annotation score1
Binding affinityMOAD: ic50=0.22uM
BindingDB: IC50=330.5nM
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:5svf, PDBe:5svf, PDBj:5svf
PDBsum5svf
PubMed28132785
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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