Structure of PDB 3k6l Chain B Binding Site BS01

Receptor Information
>3k6l Chain B (length=164) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQ
VDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALV
PRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLK
QQRIRQKVEKLDRL
Ligand information
Ligand ID2BB
InChIInChI=1S/C16H31N3O5/c1-9(2)8-10(11(20)14(22)18-24)13(21)17-12(16(3,4)5)15(23)19(6)7/h9-12,20,24H,8H2,1-7H3,(H,17,21)(H,18,22)/t10-,11+,12-/m1/s1
InChIKeyUSHCFFHZEHRVBD-GRYCIOLGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CC(C)CC(C(C(=O)NO)O)C(=O)NC(C(=O)N(C)C)C(C)(C)C
CACTVS 3.352CC(C)C[CH]([CH](O)C(=O)NO)C(=O)N[CH](C(=O)N(C)C)C(C)(C)C
CACTVS 3.352CC(C)C[C@H]([C@H](O)C(=O)NO)C(=O)N[C@H](C(=O)N(C)C)C(C)(C)C
ACDLabs 11.02O=C(NO)C(O)C(C(=O)NC(C(=O)N(C)C)C(C)(C)C)CC(C)C
OpenEye OEToolkits 1.7.0CC(C)C[C@H]([C@@H](C(=O)NO)O)C(=O)N[C@H](C(=O)N(C)C)C(C)(C)C
FormulaC16 H31 N3 O5
Name(2S,3R)-N~4~-[(1S)-1-(dimethylcarbamoyl)-2,2-dimethylpropyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide
ChEMBL
DrugBank
ZINCZINC000001542962
PDB chain3k6l Chain B Residue 170 [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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PDB3k6l The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827
Resolution2.15 Å
Binding residue
(original residue number in PDB)		E42 G43 I44 G45 Q50 E88 G89 C90 R97 L125 C129 H132 E133 H136
Binding residue
(residue number reindexed from 1)		E42 G43 I44 G45 Q50 E88 G89 C90 R97 L125 C129 H132 E133 H136
Annotation score1
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:3k6l, PDBe:3k6l, PDBj:3k6l
PDBsum3k6l
PubMed
UniProtP0A6K3|DEF_ECOLI Peptide deformylase (Gene Name=def)

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