Structure of PDB 6bkz Chain A

Receptor sequence
>6bkzA (length=412) Species: 9606 (Homo sapiens) [Search protein sequence]
KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRATDFVVPGPGKV
EITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALS
KGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLID
DMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKT
VEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKEL
AFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLG
ENLKIKLAQAKL
3D structure
PDB6bkz Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of His315.
ChainA
Resolution2.01 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 1.1.1.42: isocitrate dehydrogenase (NADP(+)).
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 NAP A T75 I76 T77 N96 S287 H309 G310 T311 V312 R314 H315 T327 N328 D375 T73 I74 T75 N94 S285 H307 G308 T309 V310 R312 H313 T325 N326 D373
BS02 DWM A A111 I113 L120 W124 I128 M259 W267 V281 A282 G284 Y285 A109 I111 L118 W122 I126 M257 W265 V279 A280 G282 Y283 MOAD: ic50=120nM
BindingDB: IC50=120nM
BS03 DWM A L120 M259 V276 L118 M257 V274 MOAD: ic50=120nM
BindingDB: IC50=120nM
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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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bkz, PDBe:6bkz, PDBj:6bkz
PDBsum6bkz
PubMed30004704
UniProtO75874|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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