6WKA

human carbonic anhydrase II bound to an inhibitor modified with azidothymidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.127 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Azidothymidine "Clicked" into 1,2,3-Triazoles: First Report on Carbonic Anhydrase-Telomerase Dual-Hybrid Inhibitors.

Berrino, E.Angeli, A.Zhdanov, D.D.Kiryukhina, A.P.Milaneschi, A.De Luca, A.Bozdag, M.Carradori, S.Selleri, S.Bartolucci, G.Peat, T.S.Ferraroni, M.Supuran, C.T.Carta, F.

(2020) J Med Chem 63: 7392-7409

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00636
  • Primary Citation of Related Structures:  
    6WKA

  • PubMed Abstract: 

    Cancer cells rely on the enzyme telomerase (EC 2.7.7.49) to promote cellular immortality. Telomerase inhibitors (i.e., azidothymidine) can represent promising antitumor agents, although showing high toxicity when administered alone. Better outcomes were observed within a multipharmacological approach instead. In this context, we exploited the validated antitumor targets carbonic anhydrases (CAs; EC 4.2.1.1) IX and XII to attain the first proof of concept on CA-telomerase dual-hybrid inhibitors. Compounds 1b , 7b , 8b , and 11b showed good in vitro inhibition potency against the CAs IX and XII, with K I values in the low nanomolar range, and strong antitelomerase activity in PC-3 and HT-29 cells (IC 50 values ranging from 5.2 to 9.1 μM). High-resolution X-ray crystallography on selected derivatives in the adduct with hCA II as a model study allowed to determine their binding modes and thus to set the structural determinants necessary for further development of compounds selectively targeting the tumoral cells.


  • Organizational Affiliation

    NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), 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
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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U4V (Subject of Investigation/LOI)
Query on U4V

Download Ideal Coordinates CCD File 
C [auth A]3'-deoxy-3'-(4-{[(4-sulfamoylphenyl)amino]methyl}-1H-1,2,3-triazol-1-yl)thymidine
C19 H23 N7 O6 S
JHJCKCYGIJXIQG-GVDBMIGSSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.198α = 90
b = 41.521β = 104.358
c = 72.018γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-02-24 
  • Deposition Author(s): Peat, T.S.

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description