Structure of PDB 5lge Chain B Binding Site BS02

Receptor Information

>5lge Chain B (length=407) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKV
EITYTVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYL
STKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAM
KSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAH
GTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANAL
EEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKL
AQAKLSL

Ligand information

Ligand ID

6VN

InChI

InChI=1S/C26H33N3O2/c1-16(2)18-6-9-20(10-7-18)27-25-28-22-13-19(24(30)31)8-11-23(22)29(25)21-12-17(3)14-26(4,5)15-21/h6-11,13,16-17,21H,12,14-15H2,1-5H3,(H,27,28)(H,30,31)/t17-,21+/m1/s1

InChIKey

GWMNDWCQEWDFPA-UTKZUKDTSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.5	CC1CC(CC(C1)(C)C)n2c3ccc(cc3nc2Nc4ccc(cc4)C(C)C)C(=O)O
OpenEye OEToolkits 2.0.5	C[C@@H]1C[C@@H](CC(C1)(C)C)n2c3ccc(cc3nc2Nc4ccc(cc4)C(C)C)C(=O)O
CACTVS 3.385	C[C@@H]1C[C@@H](CC(C)(C)C1)n2c(Nc3ccc(cc3)C(C)C)nc4cc(ccc24)C(O)=O
CACTVS 3.385	C[CH]1C[CH](CC(C)(C)C1)n2c(Nc3ccc(cc3)C(C)C)nc4cc(ccc24)C(O)=O

Formula

C26 H33 N3 O2

Name

2-[(4-propan-2-ylphenyl)amino]-1-[(1~{S},5~{S})-3,3,5-trimethylcyclohexyl]benzimidazole-5-carboxylic acid

PDB chain

5lge Chain B Residue 502 [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	5lge Pan-mutant IDH1 inhibitor BAY 1436032 for effective treatment of IDH1 mutant astrocytoma in vivo.
Resolution	2.7 Å
Binding residue (original residue number in PDB)	W124 I128 I130 H132 C269 S280 V281
Binding residue (residue number reindexed from 1)	W122 I126 I128 H130 C260 S271 V272
Annotation score	1

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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Cellular Component

External links

PDB	RCSB:5lge, PDBe:5lge, PDBj:5lge
PDBsum	5lge
PubMed	28124097
UniProt	O75874\|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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