Structure of PDB 1bsk Chain A Binding Site BS02

Receptor Information
>1bsk Chain A (length=166) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQ
VDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALV
PRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLK
QQRIRQKVEKLDRLKA
Ligand information
Ligand IDMLN
InChIInChI=1S/C18H28N3O8P/c1-4-5-6-16(29-30(26,27)28)18(23)20-15(11-12(2)3)17(22)19-13-7-9-14(10-8-13)21(24)25/h7-10,12,15-16H,4-6,11H2,1-3H3,(H,19,22)(H,20,23)(H2,26,27,28)/t15-,16-/m0/s1
InChIKeyHARXAJAHMRMERT-HOTGVXAUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCC(C(=O)NC(CC(C)C)C(=O)Nc1ccc(cc1)[N+](=O)[O-])OP(=O)(O)O
CACTVS 3.341CCCC[CH](O[P](O)(O)=O)C(=O)N[CH](CC(C)C)C(=O)Nc1ccc(cc1)[N+]([O-])=O
ACDLabs 10.04O=C(Nc1ccc(cc1)[N+]([O-])=O)C(NC(=O)C(OP(=O)(O)O)CCCC)CC(C)C
OpenEye OEToolkits 1.5.0CCCC[C@@H](C(=O)N[C@@H](CC(C)C)C(=O)Nc1ccc(cc1)[N+](=O)[O-])OP(=O)(O)O
CACTVS 3.341CCCC[C@H](O[P](O)(O)=O)C(=O)N[C@@H](CC(C)C)C(=O)Nc1ccc(cc1)[N+]([O-])=O
FormulaC18 H28 N3 O8 P
Name(S)-2-(PHOSPHONOXY)CAPROYL-L-LEUCYL-P-NITROANILIDE
ChEMBL
DrugBankDB02276
ZINCZINC000003874621
PDB chain1bsk Chain A Residue 171 [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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PDB1bsk Structural basis for the design of antibiotics targeting peptide deformylase.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		G43 I44 G45 Q50 E88 G89 L91 H132 E133 H136
Binding residue
(residue number reindexed from 1)		G43 I44 G45 Q50 E88 G89 L91 H132 E133 H136
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.12,Ki=76uM
Enzymatic activity
Catalytic site (original residue number in PDB) G45 Q50 C90 L91 H132 E133 H136
Catalytic site (residue number reindexed from 1) G45 Q50 C90 L91 H132 E133 H136
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:1bsk, PDBe:1bsk, PDBj:1bsk
PDBsum1bsk
PubMed10200158
UniProtP0A6K3|DEF_ECOLI Peptide deformylase (Gene Name=def)

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