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 |
||
- |