Structure of PDB 8ofe Chain A Binding Site BS01

Receptor Information
>8ofe Chain A (length=164) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQ
VDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALV
PRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLK
QQRIRQKVEKLDRL
Ligand information
Ligand IDVLK
InChIInChI=1S/C19H35N3O4S/c1-4-5-6-8-15(11-21(26)13-23)18(24)20-17(14(2)3)19(25)22-10-7-9-16(22)12-27/h13-17,26-27H,4-12H2,1-3H3,(H,20,24)/t15-,16?,17+/m1/s1
InChIKeyKKQZXQHPCTWHGR-SKQWJGTPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCCCC[C@H](CN(C=O)O)C(=O)N[C@@H](C(C)C)C(=O)N1CCCC1CS
CACTVS 3.385CCCCC[CH](CN(O)C=O)C(=O)N[CH](C(C)C)C(=O)N1CCCC1CS
CACTVS 3.385CCCCC[C@H](CN(O)C=O)C(=O)N[C@@H](C(C)C)C(=O)N1CCCC1CS
OpenEye OEToolkits 2.0.7CCCCCC(CN(C=O)O)C(=O)NC(C(C)C)C(=O)N1CCCC1CS
FormulaC19 H35 N3 O4 S
Name(2R)-2-[[methanoyl(oxidanyl)amino]methyl]-N-[(2S)-3-methyl-1-oxidanylidene-1-[2-(sulfanylmethyl)pyrrolidin-1-yl]butan-2-yl]heptanamide
ChEMBL
DrugBank
ZINC
PDB chain8ofe Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ofe Structural Insights into Antibacterial Payload Release from Gold Nanoparticles Bound to E. coli Peptide Deformylase.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		G43 I44 G45 Q50 G89 C90 L91 C129 H132 E133 H136
Binding residue
(residue number reindexed from 1)		G43 I44 G45 Q50 G89 C90 L91 C129 H132 E133 H136
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.88: peptide deformylase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008198 ferrous iron binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0042586 peptide deformylase activity
GO:0043022 ribosome binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0043686 co-translational protein modification
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8ofe, PDBe:8ofe, PDBj:8ofe
PDBsum8ofe
PubMed38057137
UniProtP0A6K3|DEF_ECOLI Peptide deformylase (Gene Name=def)

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