Carbonic anhydrase II in complex with nitrogenous base-bearing benezenesulfonamide

Experimental Data Snapshot

  • Resolution: 1.64 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

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This is version 1.1 of the entry. See complete history


Discovery of New Sulfonamide Carbonic Anhydrase IX Inhibitors Incorporating Nitrogenous Bases.

Nocentini, A.Bua, S.Lomelino, C.L.McKenna, R.Menicatti, M.Bartolucci, G.Tenci, B.Di Cesare Mannelli, L.Ghelardini, C.Gratteri, P.Supuran, C.T.

(2017) ACS Med Chem Lett 8: 1314-1319

  • DOI: https://doi.org/10.1021/acsmedchemlett.7b00399
  • Primary Citation of Related Structures:  
    6B59, 6B5A

  • PubMed Abstract: 

    Incorporation of the purine/pyrimidine moieties as tails to classical benzenesulfonamide scaffolds afforded two series of human (h) carbonic anhydrase (CA, EC inhibitors. The compounds were designed according to the molecular hybridization approach, in order to modulate the interaction with different CA isozymes and exploit the antitumor effect of uracil and adenine derivatives in parallel and synergic mode to the inhibition of the tumor-associated hCA IX. The sulfonamides were investigated as inhibitors of four isoforms, cytosolic hCA I/II and transmembrane hCA IV/IX. The inhibitory profiles were dependent on the length and positioning of the spacer connecting the two pharmacophores. X-ray crystallography demonstrated the binding mode of an inhibitor to hCA II and hCA IX-mimic. Compounds endowed with the best hCA IX inhibitory efficacy were evaluated for antiproliferative activity against HT-29 colon cancer cell lines. The in vitro results suggest multiple mechanisms of action are responsible for the compounds' cytotoxic efficacy.

  • Organizational Affiliation

    Department of NEUROFARBA, Pharmaceutical and Nutraceutical section, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2257Homo sapiensMutation(s): 0 
Gene Names: CA2
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
GTEx:  ENSG00000104267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
CQS BindingDB:  6B59 Ki: 8.2 (nM) from 1 assay(s)
Binding MOAD:  6B59 Ki: 8.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.64 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.646α = 90
b = 41.667β = 104.18
c = 72.633γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description