Structure of PDB 5mte Chain A Binding Site BS01

Receptor Information
>5mte Chain A (length=137) Species: 238892 (Vibrio phage VP16T) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKILKDDAPELHAIAAEVPHGEDVKDLVLDMTAAMTAAGGIGLAGNQVGV
LKRIIVLRCPTFKGCVINPIITRHTDGHVYSPEGCLSYPGKTVAKKRRNK
VVVEGYDMDWQPITIAAKGLTAFCLQHEIDHLNGVTI
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 chain5mte Chain A Residue 201 [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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PDB5mte Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		G40 I41 G42 Q47 P82 E83 G84 C85 L86 H127 E128 H131
Binding residue
(residue number reindexed from 1)		G40 I41 G42 Q47 P82 E83 G84 C85 L86 H127 E128 H131
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.78,Ki=167nM
Enzymatic activity
Catalytic site (original residue number in PDB) G42 Q47 C85 L86 H127 E128 H131
Catalytic site (residue number reindexed from 1) G42 Q47 C85 L86 H127 E128 H131
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0042586 peptide deformylase activity
GO:0046872 metal ion binding
Biological Process
GO:0018206 peptidyl-methionine modification

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Molecular Function
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Biological Process
External links
PDB RCSB:5mte, PDBe:5mte, PDBj:5mte
PDBsum5mte
PubMed29101077
UniProtQ6VT21

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