Structure of PDB 1ai3 Chain A Binding Site BS01

Receptor Information
>1ai3 Chain A (length=414) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAA
VEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGP
LTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIF
RENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCS
EEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLAREE
FGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACM
NLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVN
PGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKL
LKCSEFGDAIIENM
Ligand information
Ligand IDNDO
InChIInChI=1S/C21H27N6O18P3/c22-17(31)9-2-1-3-26(4-9)20-15(30)13(28)10(42-20)5-40-47(36,37)45-48(38,39)41-6-11-14(29)16(44-46(33,34)35)21(43-11)27-8-25-12-18(27)23-7-24-19(12)32/h1-4,7-8,10-11,13-16,20-21,28-30H,5-6H2,(H6-,22,23,24,31,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyWKSUSMNNBQFESD-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[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(O)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5O)OP(=O)(O)O)O)O)O)C(=O)N
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5O)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(O)ncnc45)[CH](O)[CH]2O
FormulaC21 H27 N6 O18 P3
NameNICOTINAMIDE-(6-DEAMINO-6-HYDROXY-ADENINE)-DINUCLEOTIDE PHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain1ai3 Chain A Residue 417 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1ai3 Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I37 G101 P102 L103 T104 A337 T338 H339 G340 T341 P343 V351 N352 Y391 D392 R395
Binding residue
(residue number reindexed from 1)		I35 G99 P100 L101 T102 A335 T336 H337 G338 T339 P341 V349 N350 Y389 D390 R393
Annotation score3
Binding affinityMOAD: Ki=403uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y160 K230 D283 D307 D311
Catalytic site (residue number reindexed from 1) Y158 K228 D281 D305 D309
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ai3, PDBe:1ai3, PDBj:1ai3
PDBsum1ai3
PubMed9211842
UniProtP08200|IDH_ECOLI Isocitrate dehydrogenase [NADP] (Gene Name=icd)

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