Structure of PDB 2pd4 Chain D Binding Site BS01

Receptor Information
>2pd4 Chain D (length=274) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFLKGKKGLIVGVANNKSIAYGIAQSCFNQGATLAFTYLNESLEKRVRPI
AQELNSPYVYELDVSKEEHFKSLYNSVKKDLGSLDFIVHSVAFAPKEALE
GSLLETSKSAFNTAMEISVYSLIELTNTLKPLLNNGASVLTLSYLGSTKY
MAHYNVMGLAKAALESAVRYLAVDLGKHHIRVNALSAGPIRTLASSGIAD
FRMILKWNEINAPLRKNVSLEEVGNAGMYLLSSLSSGVSGEVHFVDAGYH
VMGMGAVEEKDNKATLLWDLHKEQ
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 chain2pd4 Chain D Residue 4780 [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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PDB2pd4 Crystal structure of the Helicobacter pylori enoyl-acyl carrier protein reductase in complex with hydroxydiphenyl ether compounds, triclosan and diclosan
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G13 A15 S19 I20 L40 D64 V65 S91 V92 A93 I118 S144 K162 P190 I191 T193 A195
Binding residue
(residue number reindexed from 1)		G12 A14 S18 I19 L39 D63 V64 S90 V91 A92 I117 S143 K161 P189 I190 T192 A194
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y155 K162
Catalytic site (residue number reindexed from 1) Y154 K161
Enzyme Commision number 1.3.1.9: enoyl-[acyl-carrier-protein] reductase (NADH).
Gene Ontology
Molecular Function
GO:0004318 enoyl-[acyl-carrier-protein] reductase (NADH) activity
GO:0016491 oxidoreductase activity
GO:0042802 identical protein binding
Biological Process
GO:0006633 fatty acid biosynthetic process
GO:0030497 fatty acid elongation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2pd4, PDBe:2pd4, PDBj:2pd4
PDBsum2pd4
PubMed17879346
UniProtO24990|FABI_HELPY Enoyl-[acyl-carrier-protein] reductase [NADH] FabI (Gene Name=fabI)

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