PDB Entry (5lnu) |
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PDB ID: 5lnu | Resolution: 1.73 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 28092359 | DOI: 10.1038/nchembio.2273 | |
Protein |
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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 |
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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 |
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