Structure of PDB 6b0z Chain C Binding Site BS03

Receptor Information
>6b0z Chain C (length=410) 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
LKIKLAQAKL
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 C Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6b0z Discovery and Evaluation of Clinical Candidate IDH305, a Brain Penetrant Mutant IDH1 Inhibitor.
Resolution2.334 Å
Binding residue
(original residue number in PDB)		R109 A111 R119 L120 I128 I130 S278 M291
Binding residue
(residue number reindexed from 1)		R107 A109 R117 L118 I126 I128 S274 M287
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

View graph for
Molecular Function
View graph for
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)

[Back to BioLiP]