Structure of PDB 6vfz Chain B Binding Site BS01

Receptor Information

>6vfz Chain B (length=406) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

RIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDIQLKYFDLGLPNRDQT
DDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIQNI
LGGTVFREPIICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVADRAGTF
KMVFTPKDGSGVKEWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQK
KWPLYMSTKNTILKAYDGRFKDIFQEIFDKHYKTDFDKNKIWYEHRLIDD
MVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTI
EAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLI
RFAQMLEKVCVETVESGAMTKDLAGCIHGLSNVKLNEHFLNTTDFLDTIK
SNLDRA

Ligand information

Ligand ID

9UO

InChI

InChI=1S/C14H13ClF6N6/c1-6(13(16,17)18)22-11-25-10(8-4-3-5-9(15)24-8)26-12(27-11)23-7(2)14(19,20)21/h3-7H,1-2H3,(H2,22,23,25,26,27)/t6-,7-/m1/s1

InChIKey

QCZAWDGAVJMPTA-RNFRBKRXSA-N

SMILES

Software	SMILES
CACTVS 3.385	C[CH](Nc1nc(N[CH](C)C(F)(F)F)nc(n1)c2cccc(Cl)n2)C(F)(F)F
OpenEye OEToolkits 2.0.6	C[C@H](C(F)(F)F)Nc1nc(nc(n1)N[C@H](C)C(F)(F)F)c2cccc(n2)Cl
CACTVS 3.385	C[C@@H](Nc1nc(N[C@H](C)C(F)(F)F)nc(n1)c2cccc(Cl)n2)C(F)(F)F
ACDLabs 12.01	c1(nc(NC(C)C(F)(F)F)nc(n1)NC(C)C(F)(F)F)c2nc(Cl)ccc2
OpenEye OEToolkits 2.0.6	CC(C(F)(F)F)Nc1nc(nc(n1)NC(C)C(F)(F)F)c2cccc(n2)Cl

Formula

C14 H13 Cl F6 N6

Name

6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine

PDB chain

6vfz Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6vfz Vorasidenib (AG-881): A First-in-Class, Brain-Penetrant Dual Inhibitor of Mutant IDH1 and 2 for Treatment of Glioma.
Resolution	1.99 Å
Binding residue (original residue number in PDB)	W164 V297 L298 V315 Q316 I319
Binding residue (residue number reindexed from 1)	W122 V255 L256 V273 Q274 I277
Annotation score	1
Binding affinity	BindingDB: IC50=8.0nM

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:0016491	oxidoreductase activity
GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0046872	metal ion binding
GO:0051287	NAD binding

	Biological Process
GO:0005975	carbohydrate metabolic 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

	Cellular Component
GO:0005739	mitochondrion
GO:0005759	mitochondrial matrix
GO:0005777	peroxisome
GO:0005829	cytosol
GO:0070062	extracellular exosome

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Cellular Component

External links

PDB	RCSB:6vfz, PDBe:6vfz, PDBj:6vfz
PDBsum	6vfz
PubMed	32071674
UniProt	P48735\|IDHP_HUMAN Isocitrate dehydrogenase [NADP], mitochondrial (Gene Name=IDH2)

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