Structure of PDB 1npd Chain A Binding Site BS01

Receptor Information
>1npd Chain A (length=287) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDVTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFP
GAIEGLKALKMRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGY
LRGYNTDGTGHIRAIKESGFDIKGKTMVLLGAGGASTAIGAQGAIEGLKE
IKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADIL
TNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGC
KTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFG
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-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)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)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)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]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)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain1npd Chain A Residue 300 [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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PDB1npd The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G133 G134 A135 N155 R156 D158 F160 T204 K205 V206 M208 C232 Y234 M258 L259
Binding residue
(residue number reindexed from 1)		G133 G134 A135 N155 R156 D158 F160 T204 K205 V206 M208 C232 Y234 M258 L259
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.282: quinate/shikimate dehydrogenase [NAD(P)(+)].
Gene Ontology
Molecular Function
GO:0004764 shikimate 3-dehydrogenase (NADP+) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0030266 quinate 3-dehydrogenase (NAD+) activity
GO:0042803 protein homodimerization activity
GO:0052733 quinate 3-dehydrogenase (NADP+) activity
GO:0052734 shikimate 3-dehydrogenase (NAD+) activity
Biological Process
GO:0008652 amino acid biosynthetic process
GO:0009073 aromatic amino acid family biosynthetic process
GO:0009423 chorismate biosynthetic process
GO:0019632 shikimate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1npd, PDBe:1npd, PDBj:1npd
PDBsum1npd
PubMed12624088
UniProtP0A6D5|YDIB_ECOLI Quinate/shikimate dehydrogenase (Gene Name=ydiB)

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