Structure of PDB 7pjn Chain A Binding Site BS02
Receptor Information
>7pjn Chain A (length=406) Species:
9606
(Homo sapiens) [
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KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGCHAYRATDFVVPGPGKVEITY
TPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWP
LYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVA
QAMKSEGGFIWACKNYDGDVQSDFVAQGYGSLGMMTSVLVCPDGKTVEAE
AAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFA
NALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLK
IKLAQA
Ligand information
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
ChEMBL
CHEMBL407009
DrugBank
DB02338
ZINC
ZINC000008215411
PDB chain
7pjn Chain A Residue 604 [
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Receptor-Ligand Complex Structure
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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)
A74 T75 T77 N96 L288 G289 H309 G310 T311 V312 T313 R314 H315 T327 N328
Binding residue
(residue number reindexed from 1)
A72 T73 T75 N94 L282 G283 H303 G304 T305 V306 T307 R308 H309 T321 N322
Annotation score
4
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
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Biological Process
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Cellular Component
External links
PDB
RCSB:7pjn
,
PDBe:7pjn
,
PDBj:7pjn
PDBsum
7pjn
PubMed
35970853
UniProt
O75874
|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)
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