Structure of PDB 4nmy Chain B Binding Site BS01

Receptor Information

>4nmy Chain B (length=299) Species: 272563 (Clostridioides difficile 630)

SKKVTMVLDWTPNTNHTGLFVALDKGYYKEEGLDVEIVQPPESGAETLVA
TGKADFGISYQEQVTYAKTSEDPLPIKAVATVIQHNTSGFASPKEKNITT
AKDFEGKTYGGWGSPSEEAVFKAVMKKNRADFNKLKIVNTGQDDFFAAMK
TVDFAWIFEGWDAVKADLIGYDLNFIPVKDLDERLDYYTPLIISNETVLK
DNPELAKKFLKATTKGYEYAIKNPEESAKILVKHAPEVDEKLALKSQEYL
ASKYKDDAPRWGEMKDSVWNNYTSFLKEYKLIDKDMKASDAYTNEFLPQ

Ligand information

• Ligand ID: VIB
• InChI: InChI=1S/C12H17N4OS/c1-8-11(3-4-17)18-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7,17H,3-4,6H2,1-2H3,(H2,13,14,15)/q+1
• InChIKey: JZRWCGZRTZMZEH-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: n1c(c(cnc1C)C[n+]2c(c(sc2)CCO)C)N
  CACTVS 3.341: Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1
  OpenEye OEToolkits 1.5.0: Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO
• Formula: C12 H17 N4 O S
• Name: 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM;
  THIAMIN;
  VITAMIN B1
• ChEMBL: CHEMBL1547
• DrugBank: DB00152
• ZINC: ZINC000000049153
• PDB chain: 4nmy Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4nmy Crystal Structure of the Thiamin-bound form of Substrate-binding Protein of ABC Transporter from Clostridium difficile
• Resolution: 1.896 Å
• Binding residue (original residue number in PDB): W12 N15 Y62 E64 S90 W114 W158 I159 F160 W163 T191
• Binding residue (residue number reindexed from 1): W10 N13 Y60 E62 S88 W112 W156 I157 F158 W161 T189
• Annotation score: 4

Gene Ontology

Biological Process

• GO:0009228 thiamine biosynthetic process

External links

• PDB: RCSB:4nmy, PDBe:4nmy, PDBj:4nmy
• PDBsum: 4nmy
• UniProt: Q187U0