Structure of PDB 5mte Chain B Binding Site BS01

Receptor Information

>5mte Chain B (length=137) Species: 238892 (Vibrio phage VP16T)

MKILKDDAPELHAIAAEVPHGEDVKDLVLDMTAAMTAAGGIGLAGNQVGV
LKRIIVLRCPTFKGCVINPIITRHTDGHVYSPEGCLSYPGKTVAKKRRNK
VVVEGYDMDWQPITIAAKGLTAFCLQHEIDHLNGVTI

Ligand information

• Ligand ID: BB2
• InChI: InChI=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
• InChIKey: XJLATMLVMSFZBN-VYDXJSESSA-N
• SMILES:
  CACTVS 3.341: CCCCC[CH](CC(=O)NO)C(=O)N[CH](C(C)C)C(=O)N1CCC[CH]1CO
  OpenEye OEToolkits 1.5.0: CCCCCC(CC(=O)NO)C(=O)NC(C(C)C)C(=O)N1CCCC1CO
  ACDLabs 10.04: O=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
• Formula: C19 H35 N3 O5
• Name: ACTINONIN;
  2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE
• ChEMBL: CHEMBL308333
• DrugBank: DB04310
• ZINC: ZINC000003979014
• PDB chain: 5mte Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mte Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts.
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): G40 I41 G42 Q47 P82 E83 G84 C85 L86 L120 H127 E128 H131
• Binding residue (residue number reindexed from 1): G40 I41 G42 Q47 P82 E83 G84 C85 L86 L120 H127 E128 H131
• Annotation score: 1

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

Gene Ontology

Molecular Function

• GO:0042586 peptide deformylase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0018206 peptidyl-methionine modification

External links

• PDB: RCSB:5mte, PDBe:5mte, PDBj:5mte
• PDBsum: 5mte
• PubMed: 29101077
• UniProt: Q6VT21