Structure of PDB 3sw8 Chain P Binding Site BS01

Receptor Information

>3sw8 Chain P (length=194) Species: 1313 (Streptococcus pneumoniae)

SAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQ
FLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIEAYDLEAIM
YNPKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKH
RIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLILE

Ligand information

• Ligand ID: 5LI
• InChI: InChI=1S/C10H10Cl2N2O3/c11-8-3-1-2-7(9(8)12)10(16)13-4-5-14(17)6-15/h1-3,6,17H,4-5H2,(H,13,16)
• InChIKey: QOBOQKAHMKWYEE-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: Clc1c(C(=O)NCCN(O)C=O)cccc1Cl
  CACTVS 3.370: ON(CCNC(=O)c1cccc(Cl)c1Cl)C=O
  OpenEye OEToolkits 1.7.2: c1cc(c(c(c1)Cl)Cl)C(=O)NCCN(C=O)O
• Formula: C10 H10 Cl2 N2 O3
• Name: 2,3-dichloro-N-{2-[formyl(hydroxy)amino]ethyl}benzamide
• ZINC: ZINC000003818099
• PDB chain: 3sw8 Chain P Residue 205

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3sw8 Understanding the origins of time-dependent inhibition by polypeptide deformylase inhibitors.
• Resolution: 1.702 Å
• Binding residue (original residue number in PDB): G70 V71 G72 Q77 E128 G129 C130 L131 V170 H173 E174 H177
• Binding residue (residue number reindexed from 1): G69 V70 G71 Q76 E119 G120 C121 L122 V161 H164 E165 H168
• Annotation score: 1
• Binding affinity: MOAD: Ki=25910nM
  PDBbind-CN: -logKd/Ki=4.50,Ki=31.72uM

Enzymatic activity

• 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

External links

• PDB: RCSB:3sw8, PDBe:3sw8, PDBj:3sw8
• PDBsum: 3sw8
• PubMed: 21711014
• UniProt: Q939R9