PDB Entry (5lns)
PDB ID: 5lns Resolution: 1.91 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:   RIBOSE-5-PHOSPHATE (linear form)
Canonical SMILES:   O[C@H](COP(O)(O)=O)[C@@H](O)[C@@H](O)C=O
Standard InChI:   InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4+,5-/m0/s1
HET Code:   5RP PubChem:   77982
DrugBank:   DB02053 ChEMBL:   CHEMBL1235597
Molecular Formula:   C5H11O8P Mol. Weight:   230.01915 logP:   -2.6227
HBD:   5 HBA:   6
#Rotatable Bonds:   6 TPSA:   144.52
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Imine Condensation LYS 98 A 13.13 8.92 Ketone
Binding Affinity
-