PDB Entry (5lnw)
PDB ID: 5lnw Resolution: 1.9 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:   (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
-