Structure of PDB 5jf3 Chain A Binding Site BS01

Receptor Information
>5jf3 Chain A (length=203) Species: 1311 (Streptococcus agalactiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAIDKLVKASHLIDMNDIIREGNPTLRKVAEEVTFPLSEKEEILGEKMMQ
FLKHSQDPIMAEKLGLRGGVGLAAPQLDISKRIIAVLVPNVEDAQGNPPK
EAYSLQEVMYNPKVVSHSVQDAALSDGEGCLSVDREVPGYVVRHARVTIE
YFDKTGEKHRLKLKGYNSIVVQHEIDHIDGIMFYDRINEKNPFAVKEGLL
ILE
Ligand information
Ligand IDSF5
InChIInChI=1S/C18H23N3O5/c1-3-4-5-14(11-16(22)20-24)17-19-15(21-26-17)10-12-6-8-13(9-7-12)18(23)25-2/h6-9,14,24H,3-5,10-11H2,1-2H3,(H,20,22)/t14-/m1/s1
InChIKeyPKBQPXFVXNPVJM-CQSZACIVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CCCC[C@H](CC(=O)NO)c1nc(no1)Cc2ccc(cc2)C(=O)OC
CACTVS 3.385CCCC[C@H](CC(=O)NO)c1onc(Cc2ccc(cc2)C(=O)OC)n1
CACTVS 3.385CCCC[CH](CC(=O)NO)c1onc(Cc2ccc(cc2)C(=O)OC)n1
OpenEye OEToolkits 2.0.4CCCCC(CC(=O)NO)c1nc(no1)Cc2ccc(cc2)C(=O)OC
ACDLabs 12.01N(C(CC(c1onc(n1)Cc2ccc(cc2)C(=O)OC)CCCC)=O)O
FormulaC18 H23 N3 O5
Namemethyl 4-({5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl}methyl)benzoate
ChEMBL
DrugBank
ZINCZINC000584905672
PDB chain5jf3 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5jf3 A unique peptide deformylase platform to rationally design and challenge novel active compounds.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		G72 Q77 C131 L132 H174 E175 H178
Binding residue
(residue number reindexed from 1)		G71 Q76 C130 L131 H173 E174 H177
Annotation score1
Binding affinityMOAD: Ki=38nM
PDBbind-CN: -logKd/Ki=7.42,Ki=38nM
Enzymatic activity
Catalytic site (original residue number in PDB) G72 Q77 C131 L132 H174 E175 H178
Catalytic site (residue number reindexed from 1) G71 Q76 C130 L131 H173 E174 H177
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:5jf3, PDBe:5jf3, PDBj:5jf3
PDBsum5jf3
PubMed27762275
UniProtQ8E378|DEF_STRA3 Peptide deformylase (Gene Name=def)

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