Structure of PDB 3rku Chain B Binding Site BS01

Receptor Information
>3rku Chain B (length=268) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMSQGRKAAERLAKKTVLITGASAGIGKATALEYLEASNGDMKLILAARR
LEKLEELKKTIDQEFPNAKVHVAQLDITQAEKIKPFIENLPQEFKDIDIL
VNNAGKALGSDRVGQIATEDIQDVFDTNVTALINITQAVLPIFQAKNSGD
IVNLGSIAGRDAYPTGSIYCASKFAVGAFTDSLRKELINTKIRVILIAPG
LVETEFSLVRYRGNEEQAKNVYKDTTPLMADDVADLIVYATSRKQNTVIA
DTLIFPTNQASPHHIFRG
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 chain3rku Chain B Residue 268 [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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PDB3rku Substrate Fingerprint and the Structure of NADP+ Dependent Serine Dehydrogenase from Saccharomyces cerevisiae complexed with NADP+
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G20 S22 G24 I25 A47 R48 R49 D75 I76 N102 A103 G104 K105 L153 S155 Y168 K172 P198 G199 V201 T203 E204 F205
Binding residue
(residue number reindexed from 1)		G21 S23 G25 I26 A48 R49 R50 D76 I77 N103 A104 G105 K106 L154 S156 Y169 K173 P199 G200 V202 T204 E205 F206
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) A106 N127 S155 Y168 K172 N213
Catalytic site (residue number reindexed from 1) A107 N128 S156 Y169 K173 N214
Enzyme Commision number 1.1.1.-
1.1.1.381: 3-hydroxy acid dehydrogenase.
Gene Ontology
Molecular Function
GO:0004090 carbonyl reductase (NADPH) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0031132 serine 3-dehydrogenase activity
GO:0052588 diacetyl reductase ((S)-acetoin forming) (NAD+) activity
Biological Process
GO:0045149 acetoin metabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3rku, PDBe:3rku, PDBj:3rku
PDBsum3rku
PubMed
UniProtQ05016|YM71_YEAST NADP-dependent 3-hydroxy acid dehydrogenase (Gene Name=YMR226C)

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