PDB Entry (5lnu)
PDB ID: 5lnu Resolution: 1.73 Å Exp. Method: X-RAY DIFFRACTION
PMID: 28092359 DOI: 10.1038/nchembio.2273
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:   (2S)‐2‐amino‐3‐oxopent‐4‐enal
Canonical SMILES:   NC(C=O)C(=O)C=C
Standard InChI:   InChI=1S/C5H7NO2/c1-2-5(8)4(6)3-7/h2-4H,1,6H2
HET Code:   KIK PubChem:   -
DrugBank:   - ChEMBL:   -
Molecular Formula:   C5H7NO2 Mol. Weight:   113.047676 logP:   -0.7323
HBD:   1 HBA:   3
#Rotatable Bonds:   3 TPSA:   60.16
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Composite Reaction LYS 166 A 21.07 6.25 Vinyl Carbonyl
Composite Reaction LYS 98 A 10.19 8.91 Vinyl Carbonyl
Binding Affinity
-