7QNV | pdb_00007qnv

human carbonic anhydrase II bound to 3-methylbenzoselenoate

• PDB DOI: https://doi.org/10.2210/pdb7QNV/pdb

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


• Deposited: 2021-12-22 Released: 2023-01-18 
• Deposition Author(s): Angeli, A., Ferraroni, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.163 (DCC) 

Starting Model: experimental

Literature

Benzoselenoates: A novel class of carbonic anhydrase inhibitors.

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

(2022) Bioorg Chem 122: 105751-105751

• PubMed: 35344894 
• DOI: https://doi.org/10.1016/j.bioorg.2022.105751
• Primary Citation Related Structures: 
  7QNV, 7QOB


• PubMed Abstract: 
  

  A series of benzoselenoates has been prepared and their inhibitory properties against the most relevant human Carbonic Anhydrases (CAs) isoforms, among which hCA I, II, IV, VII, IX, and XII were investigated. These inhibitors were designed considering the carboxylates and mono-/dithiocarbamates as lead and led to the observation that the COSe ^- is a new zinc-binding group (ZBG) for metalloenzymes possessing zinc ions at their active site. The substitution pattern on aromatic ring of the benzoselenoates is the crucial structural element influencing selectivity towards various isoforms. We elucidated the binding mode of benzoselenoates to hCA I and hCA II by using X-ray crystallography. The negatively charged selenium atom from the new ZBG was observed coordinated to the zinc ion from the CA active site at a distance of 2.30-2.40 Å from it. Overall, these data might be useful for the development of new inhibitors with higher selectivity and efficacy for various hCAs.

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Organizational Affiliation: 
• University of Florence, Department of Chemistry "Ugo Schiff", Via della Lastruccia 3-13, I-50019, Sesto Fiorentino, Italy.
Department of Food and Drug, University of Parma, Parco Area delle Scienze, 27/A, 43124 Parma, Italy.
Department of Food and Drug, University of Parma, Parco Area delle Scienze, 27/A, 43124 Parma, Italy; NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy. Electronic address: [e-mail].
NEUROFARBA Department, 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: 29.84 kDa 
• Atom Count: 2,354 
• 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 [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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E6H (Subject of Investigation/LOI)	D [auth AAA], E [auth AAA]	3-methylbenzoselenoate C8 H8 O Se QQDFHUJSCFSCKL-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	C [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.163 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.43	α = 90
b = 41.42	β = 104.42
c = 72.13	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Angeli, A., Ferraroni, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-08-02
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description