Structure of PDB 4rkx Chain A Binding Site BS01

Receptor Information

>4rkx Chain A (length=254) Species: 864568 (Streptococcus pyogenes ATCC 10782)

QPVVKSLLNSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVAT
ATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNI
LPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKEN
FGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVID
GADGRNFYHVNWGWGGVSDGFFRLDALNPSALGTGGGAGGFNGYQSAVVG
IKPL

Ligand information

• Ligand ID: 3S9
• InChI: InChI=1S/C10H10N2O2/c11-6-7-12-10(13)14-8-9-4-2-1-3-5-9/h1-5H,7-8H2,(H,12,13)
• InChIKey: DVUXKEFDAGQPQU-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1ccc(cc1)COC(=O)NCC#N
  CACTVS 3.385: O=C(NCC#N)OCc1ccccc1
  ACDLabs 12.01: N#CCNC(=O)OCc1ccccc1
• Formula: C10 H10 N2 O2
• Name: benzyl (cyanomethyl)carbamate
• ChEMBL: CHEMBL3896749
• ZINC: ZINC000001685312
• PDB chain: 4rkx Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4rkx Identification and Co-complex Structure of a New S. pyogenes SpeB Small Molecule Inhibitor.
• Resolution: 1.59 Å
• Binding residue (original residue number in PDB): C192 V193 S280 G281 S282 Q332 G333 V334
• Binding residue (residue number reindexed from 1): C47 V48 S135 G136 S137 Q187 G188 V189
• Annotation score: 1
• Binding affinity: MOAD: Ki=8uM
  PDBbind-CN: -logKd/Ki=5.10,Ki=8uM

Enzymatic activity

• Catalytic site (original residue number in PDB): C192 H340 W357
• Catalytic site (residue number reindexed from 1): C47 H195 W212
• Enzyme Commision number: 3.4.22.10: streptopain.

Gene Ontology

Molecular Function

• GO:0008234 cysteine-type peptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:4rkx, PDBe:4rkx, PDBj:4rkx
• PDBsum: 4rkx
• PubMed: 26132413
• UniProt: A0A0M3KKW7