Structure of PDB 2d1c Chain A Binding Site BS01

Receptor Information
>2d1c Chain A (length=495) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLITTETGKKMHVLEDGRKLITVIPGDGIGPECVEATLKVLEAAKAPLAY
EVREAGASVFRRGIASGVPQETIESIRKTRVVLKGPLETPVGYGEKSANV
TLRKLFETYANVRPVREFPNVPTPYAGRGIDLVVVRENVEDLYAGIEHMQ
TPSVAQTLKLISWKGSEKIVRFAFELARAEGRKKVHCATKSNIMKLAEGT
LKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQFEVIVTTNMNGDILS
DLTSGLIGGLGFAPSANIGNEVAIFEAVHGSAPKYAGKNVINPTAVLLSA
VMMLRYLEEFATADLIENALLYTLEEGRVLTGDVVGYDRGAKTTEYTEAI
IQNLGKTPRKTQVRGYKPFRLPQVDGAIAPIVPRSRRVVGVDVFVETNLL
PEALGKALEDLAAGTPFRLKMISNRGTQVYPPTGGLTDLVDHYRCRFLYT
GEGEAKDPEILDLVSRVASRFRWMHLEKLQEFDGEPGFTKAQGED
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/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/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)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(N)ncnc45)[CH](O)[CH]2O
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(N)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)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain2d1c Chain A Residue 1002 [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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PDB2d1c Crystal Structure Of TT0538 protein from Thermus thermophilus HB8
Resolution1.8 Å
Binding residue
(original residue number in PDB)		P87 L88 E89 T90 N100 L261 G262 H280 G281 S282 A283 K285 Y286 I292 N293 D334
Binding residue
(residue number reindexed from 1)		P86 L87 E88 T89 N99 L260 G261 H279 G280 S281 A282 K284 Y285 I291 N292 D333
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y144 K191 D224 D248 D252
Catalytic site (residue number reindexed from 1) Y143 K190 D223 D247 D251
Enzyme Commision number 1.1.1.42: isocitrate dehydrogenase (NADP(+)).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004449 isocitrate dehydrogenase (NAD+) activity
GO:0004450 isocitrate dehydrogenase (NADP+) activity
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
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle
GO:0006102 isocitrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2d1c, PDBe:2d1c, PDBj:2d1c
PDBsum2d1c
PubMed
UniProtP33197|IDH_THET8 Isocitrate dehydrogenase [NADP] (Gene Name=icd)

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