8QQ9 | pdb_00008qq9

human carbonic anhydrase I in complex with 1-benzyl-3-(1-hydroxy-3,4-dihydro-1H-benzo[c][1,2]oxaborinin-7-yl)thiourea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.256 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.210 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Benzoxaborinine, New Chemotype for Carbonic Anhydrase Inhibition: Ex Novo Synthesis, Crystallography, In Silico Studies, and Anti-Melanoma Cell Line Activity.

Giovannuzzi, S.Nikitjuka, A.Angeli, A.Smietana, M.Massardi, M.L.Turati, M.Ronca, R.Bonardi, A.Nocentini, A.Ferraroni, M.Supuran, C.T.Winum, J.Y.

(2024) J Med Chem 67: 18221-18234

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01516
  • Primary Citation of Related Structures:  
    8Q6L, 8Q7G, 8QHO, 8QKZ, 8QQ9

  • PubMed Abstract: 

    The benzoxaborinine scaffold, a homologue of benzoxaborole with an additional carbon atom in the boracycle, shows significant potential in developing new therapeutic agents. This study reports the synthesis, inhibition assays against four human carbonic anhydrase (hCA, EC 4.2.1.1) isoforms, and anti-melanoma evaluation of 7-aryl(thio)ureido-substituted benzoxaborinines. Some derivatives, particularly compound 11 , exhibited potent inhibitory activity (below 65 nM) against hCA IX and XII and stronger antiproliferative effects than SLC-0111 on human melanoma cells under hypoxia. Crystallographic studies of benzoxaborinine 3 adducts with hCA I and II demonstrated the binding mode of this chemotype, revealing that although both benzoxaborinine 3 and benzoxaborole 10 share a similar zinc-binding mode, the expanded ring in benzoxaborinine led to a different orientation within the active site. These findings suggest that benzoxaborinines hold promise for designing novel carbonic anhydrase inhibitors.


  • Organizational Affiliation
    • IBMM, University of Montpellier, CNRS, ENSCM, 34293 Montpellier, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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: 2.00 Å
  • R-Value Free:  0.256 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.878α = 90
b = 69.835β = 90
c = 120.735γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata 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: 2024-10-16
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references