7ASJ | pdb_00007asj

Crystal structure for the complex of human carbonic anhydrase II and 3-(3-methyl-3-phenethylureido)benzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb7ASJ/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-10-27 Released: 2021-11-24 
• Deposition Author(s): Angeli, A., Ferraroni, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

One-Pot Procedure for the Synthesis of Asymmetric Substituted Ureido Benzene Sulfonamides as Effective Inhibitors of Carbonic Anhydrase Enzymes.

Vannozzi, G., Vullo, D., Angeli, A., Ferraroni, M., Combs, J., Lomelino, C., Andring, J., Mckenna, R., Bartolucci, G., Pallecchi, M., Lucarini, L., Sgambellone, S., Masini, E., Carta, F., Supuran, C.T.

(2022) J Med Chem 65: 824-837

• PubMed: 34958217 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c01906
• Primary Citation Related Structures: 
  7ASJ, 7RNY, 7RNZ


• PubMed Abstract: 
  

  We report a one-pot procedure for the synthesis of asymmetrical ureido-containing benzenesulfonamides based on in situ generation of the corresponding isocyanatobenezenesulfonamide species, which were trapped with the appropriate amines. A library of new compounds was generated and evaluated in vitro for their inhibition properties against a representative panel of the human (h) metalloenzymes carbonic anhydrases (EC 4.2.1.1), and the best performing compounds on the isozyme II (i.e., 7c , 9c , 11g , and 12c ) were screened for their ability to reduce the intraocular pressure in glaucomatous rabbits. In addition, the binding modes of 7c , 11f , and 11g were assessed by means of X-ray crystallography.

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Organizational Affiliation: 
• NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy.
Dipartimento di Chimica " Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy.
Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States.
NEUROFARBA Department, Section of Pharmacology and Toxicology, University of Florence, Via G. Pieraccini 6, 50139 Florence, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.8 kDa 
• Atom Count: 2,331 
• Modeled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RWH (Subject of Investigation/LOI)	E [auth A]	3-(3-methyl-3-phenethylureido)benzenesulfonamide C16 H19 N3 O3 S ODXMSWVMIFFZON-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RWH	BindingDB:  7ASJ	Ki: 1.6 (nM) from 1 assay(s)
NA	BindingDB:  7ASJ	Ki: min: 2.60e+7, max: 3.00e+8 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.356	α = 90
b = 41.257	β = 104.25
c = 72.133	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Angeli, A., Ferraroni, M.

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2022-12-07
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description