PDB Entry (5lnw) |
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PDB ID: 5lnw | Resolution: 1.9 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: (2R,3R)‐3‐{[(2S)‐1,3‐dioxopent‐4‐en‐2‐yl]amino}‐2,3‐dihydroxypropoxyphosphonic acid | ||
Canonical SMILES: O[C@@H](COP(O)(O)=O)[C@H](O)N[C@H](C=O)C(=O)C=C | ||
Standard InChI: InChI=1S/C8H14NO8P/c1-2-6(11)5(3-10)9-8(13)7(12)4-17-18(14,15)16/h2-3,5,7-9,12-13H,1,4H2,(H2,14,15,16)/t5-,7+,8+/m1/s1 | ||
HET Code: K8P | PubChem: - | |
DrugBank: - | ChEMBL: - | |
Molecular Formula: C8H14NO8P | Mol. Weight: 283.04572 | logP: -2.3128 |
HBD: 5 | HBA: 7 | |
#Rotatable Bonds: 9 | TPSA: 153.39 |
Covalent Mechanism |
Reaction Name | Residue | Chain ID | SASA | pKa | Warhead Name | Warhead Structure |
Composite Reaction | LYS 166 | A | 9.72 | 5.76 | Vinyl Carbonyl | |
Composite Reaction | LYS 98 | A | 16.09 | 8.8 | Aldehyde |
Binding Affinity |
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