BioLiP

Receptor Information

>7pjn Chain C (length=403) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGCHARATDFVVPGPGKVEITYT
PSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPL
YLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQ
AMKSEGGFIWACKNQSDFVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTV
TRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEV
SIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQA
KLL

Ligand ID

NDP

InChI

InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1

InChIKey

ACFIXJIJDZMPPO-NNYOXOHSSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341	NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341	NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N

Formula

C21 H30 N7 O17 P3

Name

NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

PDB chain

7pjn Chain C Residue 605 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	7pjn Resistance to the isocitrate dehydrogenase 1 mutant inhibitor ivosidenib can be overcome by alternative dimer-interface binding inhibitors.
Resolution	2.45 Å
Binding residue (original residue number in PDB)	T75 T77 H309 G310 T311 V312 T313 R314 H315 T327 N328
Binding residue (residue number reindexed from 1)	T73 T75 H297 G298 T299 V300 T301 R302 H303 T315 N316
Annotation score	4

Enzyme Commision number

1.1.1.42: isocitrate dehydrogenase (NADP(+)).

	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

PDB	RCSB:7pjn, PDBe:7pjn, PDBj:7pjn
PDBsum	7pjn
PubMed	35970853
UniProt	O75874\|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

[Back to BioLiP]

Structure of PDB 7pjn Chain C Binding Site BS02