PDB Entry (5lnt)
PDB ID: 5lnt Resolution: 2.32 Å Exp. Method: X-RAY DIFFRACTION
PMID: 28092359 DOI: 10.1038/nchembio.2273
Protein
Protein Name: Pyridoxal 5'-phosphate synthase subunit PDX1.1
Uniprot ID/ACC: O80448 (PDX11_ARATH) Organism: Arabidopsis thaliana (Mouse-ear cress)
Gene Symbol: PDX11 Gene ID: 818402
Protein Class: LYASE
Ligand
Ligand Name:   {[(1E)-4-amino-3-oxopenta-1,4-dien-1-yl]oxy}phosphonic acid
Canonical SMILES:   NC(=C)C(=O)\C=C\OP(O)(O)=O
Standard InChI:   InChI=1S/C5H8NO5P/c1-4(6)5(7)2-3-11-12(8,9)10/h2-3H,1,6H2,(H2,8,9,10)/b3-2+
HET Code:   KPR PubChem:   -
DrugBank:   - ChEMBL:   -
Molecular Formula:   C5H8NO5P Mol. Weight:   193.014 logP:   -0.3491
HBD:   3 HBA:   4
#Rotatable Bonds:   4 TPSA:   109.85
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Michael Addition LYS 98 A 9.18 8.69 Vinyl Carbonyl
Binding Affinity
-