Structure of PDB 4ajc Chain A Binding Site BS01

Receptor Information
>4ajc Chain A (length=415) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDA
AVEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIMG
PLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVI
FRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPC
SEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLARE
EFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIAC
MNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKV
NPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAK
LLKCSEFGDAIIENM
Ligand information
Ligand IDA2P
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(25-27(20,21)22)6(16)4(24-10)1-23-26(17,18)19/h2-4,6-7,10,16H,1H2,(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
InChIKeyAEOBEOJCBAYXBA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O[P](O)(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)OP(=O)(O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(OP(=O)(O)O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)OP(=O)(O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-2'-5'-DIPHOSPHATE
ChEMBLCHEMBL1161861
DrugBankDB02098
ZINCZINC000004096223
PDB chain4ajc 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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PDB4ajc Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		H339 G340 A342 Y345 V351 N352 Y391 D392
Binding residue
(residue number reindexed from 1)		H338 G339 A341 Y344 V350 N351 Y390 D391
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) Y160 K230 D283 D307 D311
Catalytic site (residue number reindexed from 1) Y159 K229 D282 D306 D310
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:0046872 metal ion binding
GO:0051287 NAD binding
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle
GO:0006979 response to oxidative stress
GO:0022900 electron transport chain
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ajc, PDBe:4ajc, PDBj:4ajc
PDBsum4ajc
PubMed22891681
UniProtP08200|IDH_ECOLI Isocitrate dehydrogenase [NADP] (Gene Name=icd)

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