Structure of PDB 3qbc Chain A Binding Site BS02

Receptor Information

>3qbc Chain A (length=160) Species: 158878 (Staphylococcus aureus subsp. aureus Mu50)

SHMIQAYLGLGSNIGDRESQLNDAIKILNEYDGISVSNISPIYETAPVGY
TEQPNFLNLCVEIQTTLTVLQLLECCLKTEECLHRIRKERWGPRTLDVDI
LLYGEEMIDLPKLSVPHPRMNERAFVLIPLNDIAANVVEPRSKLKVKDLV
FVDDSVKRYK

Ligand information

• Ligand ID: B55
• InChI: InChI=1S/C5H5N5OS/c6-4-8-2-1(3(11)10-4)7-5(12)9-2/h(H5,6,7,8,9,10,11,12)
• InChIKey: JHEKNTQSGTVPAO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c12c([nH]c(n1)S)N=C(NC2=O)N
  CACTVS 3.341: NC1=Nc2[nH]c(S)nc2C(=O)N1
  ACDLabs 10.04: O=C1c2nc(S)nc2N=C(N1)N
• Formula: C5 H5 N5 O S
• Name: 2-amino-8-sulfanyl-1,9-dihydro-6H-purin-6-one;
  2-amino-8-mercapto-1H-purin-6(9H)-one
• ChEMBL: CHEMBL178006
• ZINC: ZINC000006661769
• PDB chain: 3qbc Chain B Residue 163

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3qbc Structure of S. aureus HPPK and the discovery of a new substrate site inhibitor
• Resolution: 1.65 Å
• Binding residue (original residue number in PDB): P109 K110
• Binding residue (residue number reindexed from 1): P111 K112
• Annotation score: 1
• Binding affinity: MOAD: Kd=10.8uM
  PDBbind-CN: -logKd/Ki=4.97,Kd=10.8uM

Enzymatic activity

• Catalytic site (original residue number in PDB): R83 R92 D95 D97
• Catalytic site (residue number reindexed from 1): R85 R94 D97 D99
• Enzyme Commision number: 2.7.6.3: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase.

Gene Ontology

Molecular Function

• GO:0003848 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity

Biological Process

• GO:0009396 folic acid-containing compound biosynthetic process
• GO:0016310 phosphorylation
• GO:0046654 tetrahydrofolate biosynthetic process
• GO:0046656 folic acid biosynthetic process

External links

• PDB: RCSB:3qbc, PDBe:3qbc, PDBj:3qbc
• PDBsum: 3qbc
• PubMed: 22276115
• UniProt: A0A0H3JXR3