Structure of PDB 6vg0 Chain B Binding Site BS01

Receptor Information
>6vg0 Chain B (length=415) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDA
TNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRN
ILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGK
VEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMAL
SKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLI
DDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGK
TVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKE
LAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKL
GENLKIKLAQAKLSL
Ligand information
Ligand IDQWM
InChIInChI=1S/C19H23F3N6/c1-10(12-6-7-12)23-17-26-16(14-4-3-5-15(25-14)19(20,21)22)27-18(28-17)24-11(2)13-8-9-13/h3-5,10-13H,6-9H2,1-2H3,(H2,23,24,26,27,28)/t10-,11-/m1/s1
InChIKeyKRSKURCJOGAEOS-GHMZBOCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C1CC1)Nc2nc(nc(n2)NC(C)C3CC3)c4cccc(n4)C(F)(F)F
CACTVS 3.385C[CH](Nc1nc(N[CH](C)C2CC2)nc(n1)c3cccc(n3)C(F)(F)F)C4CC4
ACDLabs 12.01c4(c2nc(NC(C)C1CC1)nc(n2)NC(C3CC3)C)nc(C(F)(F)F)ccc4
CACTVS 3.385C[C@@H](Nc1nc(N[C@H](C)C2CC2)nc(n1)c3cccc(n3)C(F)(F)F)C4CC4
OpenEye OEToolkits 2.0.7C[C@H](C1CC1)Nc2nc(nc(n2)N[C@H](C)C3CC3)c4cccc(n4)C(F)(F)F
FormulaC19 H23 F3 N6
NameN~2~,N~4~-bis[(1R)-1-cyclopropylethyl]-6-[6-(trifluoromethyl)pyridin-2-yl]-1,3,5-triazine-2,4-diamine
ChEMBLCHEMBL4278828
DrugBank
ZINC
PDB chain6vg0 Chain B Residue 501 [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]
PDB6vg0 Vorasidenib (AG-881): A First-in-Class, Brain-Penetrant Dual Inhibitor of Mutant IDH1 and 2 for Treatment of Glioma.
Resolution2.66 Å
Binding residue
(original residue number in PDB)		W124 I251 Y272 D273 Q277
Binding residue
(residue number reindexed from 1)		W123 I250 Y271 D272 Q276
Annotation score1
Binding affinityBindingDB: IC50=2.0nM
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:6vg0, PDBe:6vg0, PDBj:6vg0
PDBsum6vg0
PubMed32071674
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

[Back to BioLiP]