PDB Entry (2zz6)
PDB ID: 2zz6 Resolution: 1.66 Å Exp. Method: X-RAY DIFFRACTION
PMID: 19236876 DOI: 10.1016/j.jmb.2009.02.037
Protein
Protein Name: Orotidine 5'-phosphate decarboxylase
Uniprot ID/ACC: O26232 (PYRF_METTH) Organism: Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum)
Gene Symbol: pyrF Gene ID: -
Protein Class: LYASE
Ligand
Ligand Name:   6-azido-UMP
Canonical SMILES:   O[C@@H]1[C@@H](COP(O)(O)=O)O[C@H]([C@@H]1O)n1c(cc(=O)[nH]c1=O)N=[N+]=[N-]
Standard InChI:   InChI=1S/C9H12N5O9P/c10-13-12-4-1-5(15)11-9(18)14(4)8-7(17)6(16)3(23-8)2-22-24(19,20)21/h1,3,6-8,16-17H,2H2,(H,11,15,18)(H2,19,20,21)/t3-,6-,7-,8-/m1/s1
HET Code:   6AZ PubChem:   11843561
DrugBank:   - ChEMBL:   CHEMBL463623
Molecular Formula:   C9H12N5O9P Mol. Weight:   365.03726 logP:   -1.7931
HBD:   5 HBA:   9
#Rotatable Bonds:   5 TPSA:   220.07
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Nucleophilic Aromatic Substitution LYS 72 A 22.12 9.17 Azide
Binding Affinity
Database Name Value
PDBBind Ki : 190 nM
BindingDB Ki : 190 nM , Ki : 200 nM