7P1A | pdb_00007p1a

Carbonic Anhydrase VII Sultam Based Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb7P1A/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-07-01 Released: 2021-11-17 
• Deposition Author(s): D'Ambrosio, K., De Simone, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.193 (DCC) 

Literature

Sultam based Carbonic Anhydrase VII inhibitors for the management of neuropathic pain.

Akgul, O., Lucarini, E., Mannelli, L.D.C., Ghelardini, C., D'Ambrosio, K., Buonanno, M., Monti, S.M., De Simone, G., Angeli, A., Supuran, C.T., Carta, F.

(2021) Eur J Med Chem 227: 113956-113956

• PubMed: 34731762 
• DOI: https://doi.org/10.1016/j.ejmech.2021.113956
• Primary Citation Related Structures: 
  7P1A


• PubMed Abstract: 
  

  We report a series of compounds 1-17 derived from the antiepileptic drug Sulthiame (SLT) from which both the benzenesulfonamide and the sultam moiety were retained. All compounds were tested in vitro for their inhibition activity against the human (h) Carbonic Anhydrase (CA; EC 4.2.1.1) I, II, VII, IX and XII isoforms. Among the series, derivatives 1 and 11 showed great enhancement of both inhibition potency and selectivity towards the hCA VII isoform, when compared to the reference SLT drug. The binding mode of 11 within the hCA VII active site was deciphered by means of X-ray crystallography and revealed the sultam moiety being exposed to the rim of the active site. In vivo experiments on a model of neuropathic pain induced by oxaliplatin clearly showed 11 being an effective pain relieving agent and therefore worth of further exploitation towards the validation of the hCA VII as new target for the management of neuropathies.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, 35100, Bornova, İzmir, Turkey.
NEUROFARBA Department, Section of Pharmacology and Toxicology, Università degli Studi di Firenze, Viale Pieraccini 6, 50139, Florence, Italy.
Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, 80134, Naples, Italy.
Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019, Sesto Fiorentino (Florence), Italy.
Università degli Studi di Firenze, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019, Sesto Fiorentino (Florence), Italy. Electronic address: [e-mail].

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: 31.51 kDa 
• Atom Count: 2,304 
• Modeled Residue Count: 258 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 7	A	274	Homo sapiens	Mutation(s): 2  Gene Names: CA7 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P43166 (Homo sapiens) Explore P43166  Go to UniProtKB:  P43166
PHAROS:  P43166 GTEx:  ENSG00000168748

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4IQ (Subject of Investigation/LOI)	D [auth A]	4-[2-[4-[(4-methylphenyl)methyl]-1,1-bis(oxidanylidene)-1,2,4-thiadiazinan-2-yl]ethyl]benzenesulfonamide C19 H25 N3 O4 S2 RGMYFIVOQGMVRR-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4IQ	BindingDB:  7P1A	Ki: 2.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.193 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.87	α = 90
b = 89.4	β = 90
c = 44.24	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): D'Ambrosio, K., De Simone, G.

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary