9H0W | pdb_00009h0w

Human Carbonic Anhydrase II in complex with B-Thujaplicin (2-hydroxy-4-(propan-2-yl)cyclohepta-2,4,6-trien-1-one)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

O-derivatization of natural tropolone and beta-thujaplicin leading to effective inhibitors of human carbonic anhydrases IX and XII.

Melfi, F.D'Agostino, I.Carradori, S.Carta, F.Angeli, A.Costa, G.Renzi, G.Cikos, A.Vullo, D.Resetar, J.Ferraroni, M.Baroni, C.Mancuso, F.Gitto, R.Ambrosio, F.A.Marchese, E.Torcasio, R.Amodio, N.Capasso, C.Alcaro, S.Supuran, C.T.

(2025) Eur J Med Chem 290: 117552-117552

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117552
  • Primary Citation of Related Structures:  
    9H0W

  • PubMed Abstract: 

    Herein we report the chemical derivatization of the naturally occurring Tropolone (TRP) and its related compound β-Thujaplicin (β-TJP) as well as their in vitro assessment for inhibition of the physio/pathologically relevant hCAs isoforms I, II, VA; VII, IX and XII to obtain a first set of inhibition data useful for driving selected derivatives towards appropriate biomedical exploitation. The selected compound 17β was characterized for its chemical stability and assessed for its antiproliferative activity on a multiple myeloma model and showed potent pro-apoptotic features jointly with a safe toxicity profile on healthy cells. The binding mode of β-TJP within the hCA II was assessed by means of X-ray crystallography of the hCA II/β-TJP complex and showed almost complete superposition with the hCA II/TRP adduct reported in the literature. The data produced were used to elaborate a binding prediction model of such compounds on the hCAs VA, IX, and XII which are directly connected to important diseases. Overall, the achievements reported in this work are in the sustainment of the exploitation of naturally occurring troponoloid-based structures for biomedical purposes and thus contribute to the field in extending the variety of available chemical features.


  • Organizational Affiliation
    • Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, 66100, Chieti, 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: 1.44 Å
  • R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.227α = 90
b = 41.046β = 104.26
c = 71.916γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionECS_00000017

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release