9GFX

Huma Carbonic anhydrase II in complex with trans-2-phenylvinylboronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.126 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Exploring the binding mode of phenyl and vinyl boronic acids to human carbonic anhydrases.

Esposito, D.Monti, S.M.Supuran, C.T.Winum, J.Y.De Simone, G.Alterio, V.

(2024) Int J Biol Macromol 282: 136873-136873

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.136873
  • Primary Citation of Related Structures:  
    9GFV, 9GFW, 9GFX

  • PubMed Abstract: 

    Boronic acids are an interesting but still poorly studied class of carbonic anhydrase inhibitors. Previous investigations proved that derivatives incorporating aromatic, arylalkyl, and arylalkenyl moieties are low micromolar to millimolar inhibitors for several α- and β-CAs involved in pathologic states. Here we report a high-resolution X-ray study on two classes of boronic acids (phenyl and vinyl) in complex with hCA II. Our results unambiguously clarify the binding mode of these molecules to the human carbonic anhydrase active site, which occurs through their tetrahedral anionic form, regardless of the nature of the organic scaffold. Data here presented contribute to the understanding of the inhibition mechanism of boronic acids that can be fruitfully used for the rational design of novel and effective isozyme-specific carbonic anhydrase inhibitors.


  • Organizational Affiliation

    Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche (IBB-CNR), Via Pietro Castellino, 111, 80131 Naples, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.476α = 90
b = 41.524β = 104.39
c = 72.565γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
Omodel building
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian National Research Council (CNR)ItalyJoint Bilateral Agreements CNR/CINVESTAV
Ministero dell Universita e della RicercaItalyP2022EPH87

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references