7YWT

human Carbonic Anhydrase II in complex with 4-oxo-N-(4-sulfamoylphenyl)-1,3,4,6,7,11b-hexahydro-2H-pyrazino[2,1-a]isoquinoline-2-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb7YWT/pdb

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


• Deposited: 2022-02-14 Released: 2023-02-22 
• Deposition Author(s): Angeli, A., Ferraroni, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 0.177 
• R-Value Work: 0.162 

Starting Model: experimental

Literature

Development of Praziquantel sulphonamide derivatives as antischistosomal drugs.

Angeli, A., Ferraroni, M., Carta, F., Haberli, C., Keiser, J., Costantino, G., Supuran, C.T.

(2022) J Enzyme Inhib Med Chem 37: 1479-1494

• PubMed: 35635137 
• DOI: https://doi.org/10.1080/14756366.2022.2078970
• Primary Citation of Related Structures:  
  7QZX, 7R1X, 7YWT, 7YZH


• PubMed Abstract: 
  

  The almost empty armamentarium to treat schistosomiasis, a neglected parasitic disorder caused by trematode flatworms of the genus Schistosoma , except Praziquantel (PZQ), urged to find new alternatives to fight this infection. Carbonic Anhydrase from Schistosoma mansoni (SmCA) is a possible new target against this nematode. Here, we propose new PZQ derivatives bearing a primary sulphonamide group in order to obtain hybrid drugs. All compounds were evaluated for their inhibition profiles on both humans and Schistosoma CAs, X-ray crystal data of SmCA and hCA II in adduct with some inhibitors were obtained allowing the understanding of the main structural factors responsible of activity. The compounds showed in vitro inhibition of immature and adult S. mansoni , but further optimisation is required for improved activity.

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Organizational Affiliation: 

NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, 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: 29.85 kDa 
• Atom Count: 2,380 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I6U (Subject of Investigation/LOI)	D [auth AAA]	(11~{b}~{R})-4-oxidanylidene-~{N}-(4-sulfamoylphenyl)-3,6,7,11~{b}-tetrahydro-1~{H}-pyrazino[2,1-a]isoquinoline-2-carboxamide C19 H20 N4 O4 S FKLQDIPEZBBTGO-KRWDZBQOSA-N
GOL	B [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 0.177 
• R-Value Work: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.42	α = 90
b = 41.48	β = 104.445
c = 72.04	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: 2023-02-22 
Deposition Author(s): Angeli, A., Ferraroni, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references
• Version 1.2: 2024-02-07
  Changes: Refinement description