Three dimensional structure of human carbonic anhydrase IX in complex with benzenesulfonamide

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms.

Zaksauskas, A.Capkauskaite, E.Jezepcikas, L.Linkuviene, V.Paketuryte, V.Smirnov, A.Leitans, J.Kazaks, A.Dvinskis, E.Manakova, E.Grazulis, S.Tars, K.Matulis, D.

(2020) Eur J Med Chem 185: 111825-111825

  • DOI: https://doi.org/10.1016/j.ejmech.2019.111825
  • Primary Citation of Related Structures:  
    6QN0, 6QN2, 6QN5, 6QN6, 6QNL, 6QUT, 6R6F, 6R6J, 6R6Y, 6R71

  • PubMed Abstract: 

    By applying an approach of a "ring with two tails", a series of novel inhibitors possessing high-affinity and significant selectivity towards selected carbonic anhydrase (CA) isoforms has been designed. The "ring" consists of 2-chloro/bromo-benzenesulfonamide, where the sulfonamide group is as an anchor coordinating the Zn(II) in the active site of CAs, and halogen atom orients the ring affecting the affinity and selectivity. First "tail" is a substituent containing carbonyl, carboxyl, hydroxyl, ether groups or hydrophilic amide linkage. The second "tail" contains aryl- or alkyl-substituents attached through a sulfanyl or sulfonyl group. Both "tails" are connected to the benzene ring and play a crucial role in selectivity. Varying the substituents, we designed compounds selective for CA VII, CA IX, CA XII, or CA XIV. Since due to binding-linked protonation reactions the binding-ready fractions of the compound and protein are much lower than one, the "intrinsic" affinities were calculated that should be used to study correlations between crystal structures and the thermodynamics of binding for rational drug design. The "intrinsic" affinities together with the intrinsic enthalpies and entropies of binding together with co-crystal structures were used demonstrate structural factors determining major contributions for compound affinity and selectivity.

  • Organizational Affiliation

    Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, Vilnius, LT, 10257, Lithuania.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 9
A, B, C, D
257Homo sapiensMutation(s): 1 
Gene Names: CA9G250MN
UniProt & NIH Common Fund Data Resources
Find proteins for Q16790 (Homo sapiens)
Explore Q16790 
Go to UniProtKB:  Q16790
PHAROS:  Q16790
GTEx:  ENSG00000107159 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16790
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.192α = 90
b = 152.192β = 90
c = 172.327γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Derived calculations
  • Version 1.2: 2021-10-06
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description