7QBH

Selenocarbamates as a novel prodrug-based approach towards Carbonic Anhydrase inhibition (hCA II)

• PDB DOI: https://doi.org/10.2210/pdb7QBH/pdb

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


• Deposited: 2021-11-19 Released: 2022-03-16 
• Deposition Author(s): Angeli, A., Ferraroni, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 0.177 
• R-Value Work: 0.152 

Starting Model: experimental

Literature

Selenocarbamates As a Prodrug-Based Approach to Carbonic Anhydrase Inhibition.

Angeli, A., Ferraroni, M., Capperucci, A., Tanini, D., Costantino, G., Supuran, C.T.

(2022) ChemMedChem 17: e202200085-e202200085

• PubMed: 35238480 
• DOI: https://doi.org/10.1002/cmdc.202200085
• Primary Citation of Related Structures:  
  7QBH


• PubMed Abstract: 
  

  A study on the activity of selenocarbamates as a novel chemotype acting as carbonic anhydrase (CA, EC 4.2.1.1) inhibitors is reported. Undergoing CA-mediated hydrolysis, selenocarbamates release selenolates behaving as zinc binding groups and effectively inhibiting CAs. A series of selenocarbamates characterised by high molecular diversity and complexity have been studied against different human CA isoforms such as hCA I, II, IX and XII. Selenocarbamates behave as masked selenols with potential biological applications as prodrugs for CAs inhibition-based strategies. X-ray studies provided insights into the binding mode of this novel class of CA inhibitors.

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Organizational Affiliation: 

Department NEUROFARBA, Sezione di Scienze Farmaceutiche, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.53 kDa 
• Atom Count: 2,396 
• Modelled 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 [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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AIW (Subject of Investigation/LOI)	C [auth AAA]	phenylmethaneselenol C7 H8 Se NSXOOKQXYVJEAP-UHFFFAOYSA-N
ZN	B [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 0.177 
• R-Value Work: 0.152 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.38	α = 90
b = 41.48	β = 104.531
c = 72.33	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: 2022-03-16 
Deposition Author(s): Angeli, A., Ferraroni, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2022-04-06
  Changes: Database references
• Version 1.2: 2022-06-15
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description