Structure of PDB 1xkd Chain B Binding Site BS01

Receptor Information
>1xkd Chain B (length=419) Species: 272557 (Aeropyrum pernix K1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPPCTTEELSPPPGGSLVEYSGGSLRVPDNPVVAFIRGDGVGPEVVESAL
KVVDAAVKKVGSRRIVWWELLAGHLAREKCGELLPKATLEGIRLARVALK
GPLETPVGTGYRSLNVAIRQALDLYANIRPVRYYGQPAPHKYADRVDMVI
FRENTEDVYAGIEWPHDSPEAARIRRFLAEEFGISIREDAGIGVKPISRF
ATRRLMERALEWALRNGNTVVTIMHKGNIMKYTEGAFMRWAYEVALEKFR
EHVVTEQEVQEKYGGVRPEGKILVNDRIADNMLQQIITRPWDYQVIVAPN
LNGDYISDAASALVGGIGMAAGMNMGDGIAVAEPVHGTAPKYAGKDLINP
SAEILSASLLIGEFMGWREVKSIVEYAIRKAVQSKKVTQDLARHMPGVQP
LRTSEYTETLIAYIDEADL
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 chain1xkd Chain B Residue 1003 [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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PDB1xkd Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		P109 L110 T112 N122 I324 G325 E340 H343 G344 T345 A346 K348 Y349 I355 N356 D397
Binding residue
(residue number reindexed from 1)		P102 L103 T105 N115 I317 G318 E333 H336 G337 T338 A339 K341 Y342 I348 N349 D390
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y166 K233 D287 D311 D315
Catalytic site (residue number reindexed from 1) Y159 K226 D280 D304 D308
Enzyme Commision number 1.1.1.42: isocitrate dehydrogenase (NADP(+)).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1xkd, PDBe:1xkd, PDBj:1xkd
PDBsum1xkd
PubMed15581899
UniProtQ9YE81

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