Crystal structure of human carbonic anhydrase II in complex with a benzenesulfonamide inhibitor

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

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Selective hydrophobic pocket binding observed within the carbonic anhydrase II active site accommodate different 4-substituted-ureido-benzenesulfonamides and correlate to inhibitor potency.

Pacchiano, F.Aggarwal, M.Avvaru, B.S.Robbins, A.H.Scozzafava, A.McKenna, R.Supuran, C.T.

(2010) Chem Commun (Camb) 46: 8371-8373

  • DOI: https://doi.org/10.1039/c0cc02707c
  • Primary Citation of Related Structures:  
    3MZC, 3N0N, 3N2P, 3N3J, 3N4B

  • PubMed Abstract: 

    4-Substituted-ureido benzenesulfonamides showing inhibitory activity against carbonic anhydrase (CA, EC II between 3.3-226 nM were crystallized in complex with the enzyme. Hydrophobic interactions between the scaffold of the inhibitors in different hydrophobic pockets of the enzyme were observed, explaining the diverse inhibitory range of these derivatives.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, Florida 32610, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
Gene Names: HCA2
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
P9B Binding MOAD:  3N0N Ki: 50 (nM) from 1 assay(s)
BindingDB:  3N0N Ki: min: 8, max: 50 (nM) from 2 assay(s)
PDBBind:  3N0N Ki: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 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 = 42.359α = 90
b = 41.448β = 104.24
c = 71.961γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description