PDB Entry (5k2z)
PDB ID: 5k2z Resolution: 1.8 Å Exp. Method: X-RAY DIFFRACTION
PMID: 27647886 DOI: 10.1073/pnas.1608125113
Protein
Protein Name: Pyridoxal 5'-phosphate synthase subunit PDX1.3
Uniprot ID/ACC: Q8L940 (PDX13_ARATH) Organism: Arabidopsis thaliana (Mouse-ear cress)
Gene Symbol: PDX13 Gene ID: 831738
Protein Class: LYASE
Ligand
Ligand Name:   2-azanylpenta-1,4-dien-3-one
Canonical SMILES:   NC(=C)C(=O)C=C
Standard InChI:   InChI=1S/C5H7NO/c1-3-5(7)4(2)6/h3H,1-2,6H2
HET Code:   6R3 PubChem:   129812530
DrugBank:   - ChEMBL:   -
Molecular Formula:   C5H7NO Mol. Weight:   97.052765 logP:   0.2139
HBD:   1 HBA:   2
#Rotatable Bonds:   2 TPSA:   43.09
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Michael Addition LYS 165 A 22.76 6.28 Vinyl Carbonyl
Michael Addition LYS 97 A 10.49 8.27 Vinyl Carbonyl
Binding Affinity
-