9G38 | pdb_00009g38

CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH SALVIANOLIC ACID P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.157 (Depositor), 0.162 (DCC) 
  • R-Value Work: 
    0.135 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 
    0.136 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IH2Click on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Depsides from Origanum dictamnus and Satureja pilosa as selective inhibitors of carbonic anhydrases: Isolation, structure elucidation, X-ray crystallography.

Paloukopoulou, C.Ntagli, O.S.Gherardi, L.Dourdouni, V.Filippou, G.Alterio, V.Giovannuzzi, S.Massardi, M.L.De Simone, G.Ronca, R.Supuran, C.T.Pescitelli, G.Karioti, A.

(2025) Arch Pharm (Weinheim) 358: e2400823-e2400823

  • DOI: https://doi.org/10.1002/ardp.202400823
  • Primary Citation of Related Structures:  
    9G38

  • PubMed Abstract: 

    In this study, four depsides were isolated from Origanum dictamnus L. and Satureja pilosa Velen. medicinal plants and their structures were assessed by means of one-dimensional (1D)- and two-dimensional (2D)-nuclear magnetic resonance, high resolution mass spectrometry, and electronic circular dichroism analyses. The compound 1, herein reported for the first time, salvianolic acid P 2, clinopodic acid I 3, and clinopodic acid O 4 were all profiled in vitro on a panel of human (h) expressed carbonic anhydrases (CAs; EC 4.2.1.1) and preferential inhibition for the tumor-associated human carbonic anhydrase (hCA) IX and hCA XII over the constitutively expressed hCA I and hCA II isoforms was observed. X-ray crystallography allowed us to assess the binding mode of salvianolic acid P 2 to hCA II. The compounds exhibited significant cytotoxic effects on the human triple-negative breast cancer cell line MDA-MB-231, suggesting that this class of depsides are promising molecules for future investigation.


  • Organizational Affiliation

    Laboratory of Pharmacognosy, Department of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2262Homo 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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.157 (Depositor), 0.162 (DCC) 
  • R-Value Work:  0.135 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 0.136 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.222α = 90
b = 41.268β = 104.37
c = 72.101γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-3000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IH2Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItalyPRIN201744BN5T

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release