PDB Entry (2zz4)
PDB ID: 2zz4 Resolution: 1.67 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-cyano-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)C#N
Standard InChI:   InChI=1S/C10H12N3O9P/c11-2-4-1-6(14)12-10(17)13(4)9-8(16)7(15)5(22-9)3-21-23(18,19)20/h1,5,7-9,15-16H,3H2,(H,12,14,17)(H2,18,19,20)/t5-,7-,8-,9-/m1/s1
HET Code:   6CN PubChem:   16666397
DrugBank:   - ChEMBL:   CHEMBL512577
Molecular Formula:   C10H12N3O9P Mol. Weight:   349.03113 logP:   -2.86322
HBD:   5 HBA:   9
#Rotatable Bonds:   4 TPSA:   195.1
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Nucleophilic Aromatic Substitution LYS 72 A 19.13 6.73 Nitrile
Binding Affinity
Database Name Value
BindingDB Ki : 29000 nM