Structure of PDB 3pa8 Chain A Binding Site BS01

Receptor Information

>3pa8 Chain A (length=245) Species: 272563 (Clostridioides difficile 630)

DFSQNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFA
KTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLT
FIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCN
MFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSE
GRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNL

Ligand information

• Ligand ID: 621
• InChI: InChI=1S/C14H25N3O6/c1-8(2)4-10(12(21)7-19)17-14(23)11(6-18)16-13(22)5-15-9(3)20/h8,10-11,18-19H,4-7H2,1-3H3,(H,15,20)(H,16,22)(H,17,23)/t10-,11-/m0/s1
• InChIKey: XARLKHLSACMNTN-QWRGUYRKSA-N
• SMILES:
  ACDLabs 12.01: O=C(NC(C(=O)CO)CC(C)C)C(NC(=O)CNC(=O)C)CO
  OpenEye OEToolkits 1.7.0: CC(C)C[C@@H](C(=O)CO)NC(=O)[C@H](CO)NC(=O)CNC(=O)C
  CACTVS 3.370: CC(C)C[C@H](NC(=O)[C@H](CO)NC(=O)CNC(C)=O)C(=O)CO
  OpenEye OEToolkits 1.7.0: CC(C)CC(C(=O)CO)NC(=O)C(CO)NC(=O)CNC(=O)C
  CACTVS 3.370: CC(C)C[CH](NC(=O)[CH](CO)NC(=O)CNC(C)=O)C(=O)CO
• Formula: C14 H25 N3 O6
• Name: N-acetylglycyl-N-[(3S)-1-hydroxy-5-methyl-2-oxohexan-3-yl]-L-serinamide
• ZINC: ZINC000058627065
• PDB chain: 3pa8 Chain A Residue 300

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3pa8 Rational design of inhibitors and activity-based probes targeting Clostridium difficile virulence factor TcdB.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): I46 H110 C155 V201 R202
• Binding residue (residue number reindexed from 1): I40 H104 C149 V195 R196
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.75,IC50=1.78uM

Enzymatic activity

• Enzyme Commision number: 2.4.1.-

External links

• PDB: RCSB:3pa8, PDBe:3pa8, PDBj:3pa8
• PDBsum: 3pa8
• PubMed: 21095570
• UniProt: Q189K3