7ZCY image
Deposition Date 2022-03-29
Release Date 2023-04-19
Last Version Date 2025-10-01
Entry Detail
PDB ID:
7ZCY
Keywords:
Title:
Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.54 Å
R-Value Free:
0.15
R-Value Work:
0.13
R-Value Observed:
0.13
Space Group:
P 63 2 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Urease subunit gamma
Gene (Uniprot):ureA
Chain IDs:A
Chain Length:100
Number of Molecules:1
Biological Source:Sporosarcina pasteurii
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Urease subunit beta
Gene (Uniprot):ureB
Chain IDs:B
Chain Length:122
Number of Molecules:1
Biological Source:Sporosarcina pasteurii
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Urease subunit alpha
Gene (Uniprot):ureC
Chain IDs:C
Chain Length:570
Number of Molecules:1
Biological Source:Sporosarcina pasteurii
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CXM A MET modified residue
KCX C LYS modified residue
Primary Citation
Optimized Ebselen-Based Inhibitors of Bacterial Ureases with Nontypical Mode of Action.
J.Med.Chem. 66 2054 2063 (2023)
PMID: 36661843 DOI: 10.1021/acs.jmedchem.2c01799

Abstact

Screening of 25 analogs of Ebselen, diversified at the N-aromatic residue, led to the identification of the most potent inhibitors of Sporosarcina pasteurii urease reported to date. The presence of a dihalogenated phenyl ring caused exceptional activity of these 1,2-benzisoselenazol-3(2H)-ones, with Ki value in a low picomolar range (<20 pM). The affinity was attributed to the increased π-π and π-cation interactions of the dihalogenated phenyl ring with αHis323 and αArg339 during the initial step of binding. Complementary biological studies with selected compounds on the inhibition of ureolysis in whole Proteus mirabilis cells showed a very good potency (IC50 < 25 nM in phosphate-buffered saline (PBS) buffer and IC90 < 50 nM in a urine model) for monosubstituted N-phenyl derivatives. The crystal structure of S. pasteurii urease inhibited by one of the most active analogs revealed the recurrent selenation of the Cys322 thiolate, yielding an unprecedented Cys322-S-Se-Se chemical moiety.

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Primary Citation of related structures