8QGV | pdb_00008qgv

Human Carbonic Anhydrase I in complex with 4-(5-acetyl-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidin-4-yl)benzenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.240 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.206 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Benzenesulfonamide decorated dihydropyrimidin(thi)ones: carbonic anhydrase profiling and antiproliferative activity.

Aslan, H.Renzi, G.Angeli, A.D'Agostino, I.Ronca, R.Massardi, M.L.Tavani, C.Carradori, S.Ferraroni, M.Governa, P.Manetti, F.Carta, F.Supuran, C.T.

(2024) RSC Med Chem 15: 1929-1941

  • DOI: https://doi.org/10.1039/d4md00101j
  • Primary Citation Related Structures: 
    8QGV

  • PubMed Abstract: 

    In the last decades, carbonic anhydrases (CAs) have become the top investigated innovative pharmacological targets and, in particular, isoforms IX and XII have been widely studied due to the evidence of their overexpression in hypoxic tumors. The frantic race to find new anticancer agents places the quick preparation of large libraries of putative bioactive compounds as the basis of a successful drug discovery and development programme. In this context, multi-component and, in general, one-step reactions are becoming very popular and, among them, Biginelli's reaction gave clean and easy-to-isolate products. Thus, we synthesized a series of Biginelli's products (10-17a-b) and similar derivatives (20-21) bearing the benzenesulfonamide moiety, which is known to inhibit CA enzymes. Through the stopped-flow technique, we were able to assess their ability to inhibit the targeted CAs IX and XII in the nanomolar range with promising selectivity over the physiologically relevant isoforms I and II. Crystallography studies and docking simulations helped us to gain insight into the interaction patterns established in the enzyme-inhibitor complex. From a chemical similarity-based screening of in-house libraries of compounds, a diphenylpyrimidine (23) emerged. The surprisingly potent inhibitory activity of 23 for CAs IX and XII along with its strong antiproliferative effect on two (triple-negative breast cancer MDA-MB-231 and glioblastoma U87MG) cell lines laid the foundation for further investigation, again confirming the key role of CAs in cancer.


  • Organizational Affiliation
    • Department of Chemistry, Faculty of Science and Arts, Sinop University Sinop Turkey hakaslan@gmail.com.

Macromolecule Content 

  • Total Structure Weight: 58.62 kDa 
  • Atom Count: 4,292 
  • Modeled Residue Count: 512 
  • Deposited Residue Count: 522 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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: 1.84 Å
  • R-Value Free:  0.240 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.206 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.94α = 90
b = 71.14β = 90
c = 120.92γ = 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: 2024-09-11
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references, Structure summary