9FAI | pdb_00009fai

Human carbonic anhydrase II complexed with 2-hydroselenobenzoic acid

• PDB DOI: https://doi.org/10.2210/pdb9FAI/pdb

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


• Deposited: 2024-05-10 Released: 2025-05-21 
• Deposition Author(s): Angeli, A., Ferraroni, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.152 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.113 (Depositor) 

Starting Model: experimental

Literature

Study of Chalcogen Aspirin Derivatives with Carbonic Anhydrase Inhibitory Properties for Treating Inflammatory Pain.

Lucarini, E., D'Antogiovanni, V., Antonioli, L., Ghelardini, C., Di Cesare Mannelli, L., Ferraroni, M., Locuoco, M., Capperucci, A., Tanini, D., Angeli, A., Supuran, C.T.

(2024) ACS Med Chem Lett 15: 1559-1565

• PubMed: 39291024 
• DOI: https://doi.org/10.1021/acsmedchemlett.4c00284
• Primary Citation Related Structures: 
  9FAI, 9FAO


• PubMed Abstract: 
  

  Carbonic anhydrase (CA) inhibitors represent intriguing tools for treating pain. This study aims at studying the pharmacological profile of chalcogen bioisosteres of aspirin, as inhibitors of CA isoforms (hCA I, II, IV, VII, IX, and XII). Our results show that selenoaspirin ( 5 ) displayed markedly superior inhibitory potency across all tested isoforms compared to thioaspirin ( 7 ) and aspirin, with a strong selectivity against the isoform CA IX. X-ray crystallography confirmed that both compounds bind effectively within the active site of hCA II, revealing unique structural characteristics compared to those of aspirin. In a preclinical model of inflammatory pain, compound 7 exhibited a longer lasting antihyperalgesic effect than aspirin, though with a lower potency. Conversely, compound 5 exhibited both lower potency and efficacy than aspirin in reducing pain, which entailed both adverse effects. Nevertheless, the therapeutic potential of chalcogen-based aspirin derivatives as novel CA inhibitors deserves to be further explored for clinical applications.

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Organizational Affiliation: 
• Department of Neuroscience, Psychology, Drug Research and Child Health, Neurofarba, Pharmacology and Toxicology Section, University of Florence, 6-50139 Florence, Italy.
Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy.
Department of Chemistry "Ugo Schiff" (DICUS), University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, I-50019 Florence, Italy.
NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 29.68 kDa 
• Atom Count: 2,420 
• Modeled Residue Count: 259 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A [auth AAA]	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IBT (Subject of Investigation/LOI)	E [auth AAA]	2-selanylbenzoic acid C7 H6 O2 Se UYXHJPFMESJIIY-UHFFFAOYSA-N
ZN	D [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth AAA]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.152 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.113 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.39	α = 90
b = 41.31	β = 104.139
c = 72.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Angeli, A., Ferraroni, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release
  
• Version 1.1: 2025-12-03
  Changes: Database references