9H81 | pdb_00009h81

human carbonic anhydrase I in complex with Sonepiprazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.262 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.202 (DCC) 

Starting Model: experimental
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Literature

Structural Studies of the Dopamine D 4 Receptor Antagonist Sonepiprazole as an Inhibitor of Human Carbonic Anhydrases.

Angeli, A.Ferraroni, M.Capasso, C.Supuran, C.T.

(2025) ACS Med Chem Lett 16: 483-486

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00034
  • Primary Citation of Related Structures:  
    9H81

  • PubMed Abstract: 

    In this study, we provide the first evidence that sonepiprazole, a dopamine D 4 receptor antagonist, acts as a potent inhibitor of human carbonic anhydrases (hCAs). Sonepiprazole exhibited significant inhibitory activity across the panel of catalytically active hCAs, with the exception of hCA IV, and hCA III. The most potent inhibition was observed against the brain-associated isoform hCA VII, with a K I of 2.9 nM. Insights from X-ray crystallographic structures of the complexes with hCA I, hCA II, and hCA XII revealed that the sulfonamide group of sonepiprazole coordinates the zinc ion in the active site, a typical interaction for this class of inhibitors. Despite the presence of isoform-specific residues at the rim of the active site pocket, these variations seem not to significantly impact the compound overall inhibition potency. These findings highlight a dual functionality of sonepiprazole as both a D 4 receptor antagonist and a carbonic anhydrase inhibitor.


  • Organizational Affiliation
    • NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 1A [auth AAA],
B [auth BBB]
261Homo sapiensMutation(s): 0 
Gene Names: CA1
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens)
Explore P00915 
Go to UniProtKB:  P00915
PHAROS:  P00915
GTEx:  ENSG00000133742 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00915
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.262 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.202 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.625α = 90
b = 71.232β = 90
c = 121.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release