The crystal structure of human carbonic anhydrase VII in complex with 4-[(4-fluorophenyl)methyl]-1-piperazinyl]benzenesulfonamide.

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 

Starting Model: experimental
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Exploring structural properties of potent human carbonic anhydrase inhibitors bearing a 4-(cycloalkylamino-1-carbonyl)benzenesulfonamide moiety.

Buemi, M.R.Di Fiore, A.De Luca, L.Angeli, A.Mancuso, F.Ferro, S.Monti, S.M.Buonanno, M.Russo, E.De Sarro, G.De Simone, G.Supuran, C.T.Gitto, R.

(2018) Eur J Med Chem 163: 443-452

  • DOI: https://doi.org/10.1016/j.ejmech.2018.11.073
  • Primary Citation of Related Structures:  
    6H2Z, 6H33, 6H34, 6H36, 6H37, 6H38

  • PubMed Abstract: 

    Guided by the crystal structure of 4-(3,4-dihydroquinolin-1(2H)-ylcarbonyl)benzenesulfonamide 3 in complex with hCA II (PDB code 4Z0Q), a novel series of cycloalkylamino-1-carbonylbenzenesulfonamides was designed and synthesized. Thus, we replaced the quinoline ring with an azepine/piperidine/piperazine nucleus and introduced further modifications on cycloalkylamine nucleus by means the installation of hydrophobic/hydrophilic functionalities able to establish additional contacts in the middle area of the enzyme cavity. Among the synthesized compounds, the derivatives 7a, 7b, 8b exhibited a remarkable inhibition for hCA II and the brain-expressed hCA VII in subnanomolar range. The binding of these molecules to the target enzymes was characterized by means of a crystallographic analysis, providing a clear snapshot of the most important interactions established by this class of inhibitors into the hCA II and hCA VII catalytic site. Notably, our results showed that the benzylpiperazine tail of compound 8b is oriented both in hCA II and in hCA VII toward a poorly explored region of the active site. These features should be further investigated for the design of new isoform selective CA inhibitors.

  • Organizational Affiliation

    Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo didattico SS, Annunziata, 98168, Messina, Italy.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 7274Homo sapiensMutation(s): 2 
Gene Names: CA7
UniProt & NIH Common Fund Data Resources
Find proteins for P43166 (Homo sapiens)
Explore P43166 
Go to UniProtKB:  P43166
GTEx:  ENSG00000168748 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43166
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.1α = 90
b = 89.24β = 90
c = 44.2γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description