PDB Entry (4c5l)
PDB ID: 4c5l Resolution: 1.85 Å Exp. Method: X-RAY DIFFRACTION
PMID: 24601602 DOI: 10.1021/JA411785R
Protein
Protein Name: Phosphomethylpyrimidine kinase
Uniprot ID/ACC: A0A0H3JTP0 (A0A0H3JTP0_STAAM) Organism: Staphylococcus aureus (strain Mu50 / ATCC 700699)
Gene Symbol: SAV0580 Gene ID: -
Protein Class: HYDROLASE
Ligand
Ligand Name:   Pyridoxal
Canonical SMILES:   Cc1ncc(CO)c(C=O)c1O
Standard InChI:   InChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3
HET Code:   UEG PubChem:   1050
DrugBank:   DB00147 ChEMBL:   CHEMBL102970
Molecular Formula:   C8H9NO3 Mol. Weight:   167.05824 logP:   0.40042
HBD:   2 HBA:   4
#Rotatable Bonds:   2 TPSA:   70.42
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Hemi(thio)acetalization CYS 110 A 31.72 13.25 Aldehyde
Binding Affinity
-