Structure of PDB 4e9b Chain A Binding Site BS02

Receptor Information
>4e9b Chain A (length=163) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALLEIIHYPSKILRTISKEVVSFDAKLHQQLDDMYETMIASEGIGLAAIQ
VGLPLRMLIINLPQEDGVQHKEDCLEIINPKFIETGGSMMYKEGCLSVPG
FYEEVERFEKVKIEYQNRFAEVKVLEASELLAVAIQHEIDHLNGVLFVDK
LSILKRKKFEKEL
Ligand information
Ligand IDBB2
InChIInChI=1S/C19H35N3O5/c1-4-5-6-8-14(11-16(24)21-27)18(25)20-17(13(2)3)19(26)22-10-7-9-15(22)12-23/h13-15,17,23,27H,4-12H2,1-3H3,(H,20,25)(H,21,24)/t14-,15+,17+/m1/s1
InChIKeyXJLATMLVMSFZBN-VYDXJSESSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCC[CH](CC(=O)NO)C(=O)N[CH](C(C)C)C(=O)N1CCC[CH]1CO
OpenEye OEToolkits 1.5.0CCCCCC(CC(=O)NO)C(=O)NC(C(C)C)C(=O)N1CCCC1CO
ACDLabs 10.04O=C(N1C(CO)CCC1)C(NC(=O)C(CC(=O)NO)CCCCC)C(C)C
CACTVS 3.341
OpenEye OEToolkits 1.5.0		CCCCC[C@H](CC(=O)NO)C(=O)N[C@@H](C(C)C)C(=O)N1CCC[C@H]1CO
FormulaC19 H35 N3 O5
NameACTINONIN;
2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE
ChEMBLCHEMBL308333
DrugBankDB04310
ZINCZINC000003979014
PDB chain4e9b Chain A Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4e9b Identification of Novel Peptide Deformylase Inhibitors from Natural Products
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G44 I45 G46 Q51 K93 G95 C96 L97 H138 E139 H142
Binding residue
(residue number reindexed from 1)		G43 I44 G45 Q50 K92 G94 C95 L96 H137 E138 H141
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G46 Q51 C96 L97 H138 E139 H142
Catalytic site (residue number reindexed from 1) G45 Q50 C95 L96 H137 E138 H141
Enzyme Commision number 3.5.1.88: peptide deformylase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0042586 peptide deformylase activity
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0018206 peptidyl-methionine modification

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4e9b, PDBe:4e9b, PDBj:4e9b
PDBsum4e9b
PubMed
UniProtQ672W7

[Back to BioLiP]