Structure of PDB 3clh Chain A Binding Site BS01

Receptor Information
>3clh Chain A (length=308) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ILIPLKEKNYKVFLGELPEIKLKQKALIISDSIVAGLHLPYLLERLKALE
VRVCVIESGEKYKNFHSLERILNNAFEMQLNRHSLMIALGGGVISDMVGF
ASSIYFRGIDFINIPTTLLAQVDASVGGKTGINTPYGKNLIGSFHQPKAV
YMDLAFLKTLEKREFQAGVAEIIKMAVCFDKNLVERLETKDLKDCLEEVI
FQSVNIKAQVVRAGLNYGHTFGHAIEKETDYERFLHGEAIAIGMRMANDL
ALSLGMLTLKEYERIENLLKKFDLIFHYKFILPKGVGAFEVASHIPKETI
IKVLEKWH
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 chain3clh Chain A Residue 400 [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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PDB3clh Structure-based inhibitor discovery of Helicobacter pylori dehydroquinate synthase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I36 V37 H41 S61 E63 K66 G94 G95 V96 D99 T119 T120 L122 D126 A127 K132 N142 T162 L163 E167
Binding residue
(residue number reindexed from 1)		I33 V34 H38 S58 E60 K63 G91 G92 V93 D96 T116 T117 L119 D123 A124 K129 N139 T159 L160 E164
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R110 K132 E174 K210 R224 N228 H231 H235 H248
Catalytic site (residue number reindexed from 1) R107 K129 E171 K207 R212 N216 H219 H223 H236
Enzyme Commision number 4.2.3.4: 3-dehydroquinate synthase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003856 3-dehydroquinate synthase activity
GO:0016829 lyase activity
GO:0016838 carbon-oxygen lyase activity, acting on phosphates
GO:0046872 metal ion binding
Biological Process
GO:0008652 amino acid biosynthetic process
GO:0009073 aromatic amino acid family biosynthetic process
GO:0009423 chorismate biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3clh, PDBe:3clh, PDBj:3clh
PDBsum3clh
PubMed18503755
UniProtP56081|AROB_HELPY 3-dehydroquinate synthase (Gene Name=aroB)

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