Structure of PDB 5vcp Chain D Binding Site BS02

Receptor Information
>5vcp Chain D (length=159) Species: 266265 (Paraburkholderia xenovorans LB400) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIREILKMGDPRLLRIADPVDHFDTPELHELVKDMFETMHDANGAGLAAP
QIGVNLQVVIFGFPVPETVLINPTITPVSQDMEEGWEGCLSVPGLRGAVS
RFSMIKYHGFDQYGKPIDRVAEGFHARVVQHECDHLIGKLYPMRINDFAK
FGFTEVLFP
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 chain5vcp Chain D Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vcp Crystal structure of a peptide deformylase from Burkholderia xenovorans in complex with actinonin
Resolution1.95 Å
Binding residue
(original residue number in PDB)		A45 G46 Q51 G98 C99 R106 H141 E142 H145
Binding residue
(residue number reindexed from 1)		A45 G46 Q51 G88 C89 R96 H131 E132 H135
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G46 Q51 C99 L100 H141 E142 H145
Catalytic site (residue number reindexed from 1) G46 Q51 C89 L90 H131 E132 H135
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:5vcp, PDBe:5vcp, PDBj:5vcp
PDBsum5vcp
PubMed
UniProtQ13XB1

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