6WKA | pdb_00006wka

human carbonic anhydrase II bound to an inhibitor modified with azidothymidine

• PDB DOI: https://doi.org/10.2210/pdb6WKA/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-15 Released: 2021-02-24 
• Deposition Author(s): Peat, T.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.166 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.127 (Depositor) 

Starting Model: experimental

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

• PubMed: 32463228 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c00636
• Primary Citation 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.

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Organizational Affiliation: 
• NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy.
Institute of Biomedical Chemistry, Pogodinskaya st. 10/8, 119121 Moscow, Russia.
Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya st. 6, 117198 Moscow, Russia.
Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy.
CSIRO, 343 Royal Parade, Parkville, Victoria 3052, Australia.
Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3-13, 50019 Sesto Fiorentino (Florence), Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.83 kDa 
• Atom Count: 2,613 
• Modeled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U4V (Subject of Investigation/LOI)	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	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
U4V	BindingDB:  6WKA	Ki: 33 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.166 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.127 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.198	α = 90
b = 41.521	β = 104.358
c = 72.018	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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