Structure of PDB 7lou Chain B Binding Site BS02

Receptor Information

>7lou Chain B (length=540) Species: 1496 (Clostridioides difficile)

SLVNRKQLEKMANVRFRTQEDEYVAILDALEEYHNMSENTVVEKYLKLKD
INSLTDIYIDTYKKSGRNKALKKFKEYLVTEVLELKNNNLTPVEKNLHFV
WIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTVVESAIN
DTLESFRENLNDPRFDYNKFFRKRMEIIYDKQKNFINYYKAQREENPELI
IDDIVKTYLSNEYSKEIDELNTYIEESLNKITQNSGNDVRNFEEFKNGES
FNLYEQELVERWNLAAASDILRISALKEIGGMYLDVDMLPGIQPDLFESI
EKPSSVTVDFWEMTKLEAIMKYKEYIPEYTSEHFDMLDEEVQSSFESVLA
SKSDKSEIFSSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNLIVK
QIENRYKILNNSLNPAISEDNDFNTTTNTFIDSIMAEANADNGRFMMELG
KYLRVGFFPDVKTTINLSGPEAYAAAYQDLLMFKEGSMNIHLIEADLRNF
EISKTNISQSTEQEMASLWSFDDARAKAQFEEYKRNYFEG

Ligand information

• Ligand ID: IFM
• InChI: InChI=1S/C6H13NO3/c8-3-4-1-7-2-5(9)6(4)10/h4-10H,1-3H2/t4-,5-,6-/m1/s1
• InChIKey: QPYJXFZUIJOGNX-HSUXUTPPSA-N
• SMILES:
  CACTVS 3.341: OC[CH]1CNC[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H]([C@@H](CN1)O)O)CO
  ACDLabs 10.04: OC1C(CO)CNCC1O
  CACTVS 3.341: OC[C@H]1CNC[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C1C(C(C(CN1)O)O)CO
• Formula: C6 H13 N O3
• Name: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE;
  Afegostat;
  isofagomine;
  (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL
• ChEMBL: CHEMBL206468
• DrugBank: DB04545
• ZINC: ZINC000003813668
• PDB chain: 7lou Chain B Residue 612

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lou Inhibition of Clostridium difficile TcdA and TcdB toxins with transition state analogues.
• Resolution: 1.82 Å
• Binding residue (original residue number in PDB): D270 R273 D286 N384 T465
• Binding residue (residue number reindexed from 1): D269 R272 D285 N383 T464
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.4.1.-
  3.4.22.-

Gene Ontology

Molecular Function

• GO:0016757 glycosyltransferase activity

External links

• PDB: RCSB:7lou, PDBe:7lou, PDBj:7lou
• PDBsum: 7lou
• PubMed: 34725358
• UniProt: P18177|TCDB_CLODI Toxin B (Gene Name=tcdB)