8R2F | pdb_00008r2f

human carbonic anhydrase II in complex with 4-(((dimethoxyphosphoryl)(4-((dimethoxyphosphoryl)((4-sulfamoylphenyl)amino)methyl)phenyl)methyl)amino)phenyl sulfuramidite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.170 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.145 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Sulfonamide-incorporated bis( alpha-aminophosphonates) as promising carbonic anhydrase inhibitors: Design, synthesis, biological evaluation, and X-ray crystallographic studies.

Sobati, M.Abdoli, M.Angeli, A.Bonardi, A.Ferraroni, M.Supuran, C.T.Zalubovskis, R.

(2024) Arch Pharm (Weinheim) 357: e2400038-e2400038

  • DOI: https://doi.org/10.1002/ardp.202400038
  • Primary Citation Related Structures: 
    8R2F

  • PubMed Abstract: 

    A novel series of sulfonamide-incorporated bis(α-aminophosphonates) acting as effective carbonic anhydrase (CA, EC 4.2.1.1) inhibitors is reported. The synthesized bivalent ligands were tested against five human (h) isoforms, hCA I, hCA II, hCA VII, hCA IX, and hCA XIII. Such derivatives showed high activity and selectivity against the cancer-related, membrane-bound isoform hCA IX, and among them, compound 5h, tetraisopropyl (1,3-phenylenebis{[(4-sulfamoylphenyl)amino]methylene})bis(phosphonate) showed a K I of 15.1 nM, being highly selective against this isoform over all other investigated ones (hCA I/IX = 42; hCA II/IX = 6, hCA VII/IX = 3, hCA XIII/IX = 5). Therefore, compound 5h could be a potential lead for the development of selective anticancer agents. The newly developed sulfonamides were also found effective inhibitors against the cytosolic hCA XIII isoform. Compound 5i displayed the best inhibition against this isoform with a K I of 17.2 nM, equal to that of the well-known inhibitor acetazolamide (AAZ), but significantly more selective over all other tested isoforms (hCA I/XIII = 239; hCA II/XIII = 23, hCA VII/XIII = 2, hCA IX/XIII = 3) compared to AAZ.


  • Organizational Affiliation
    • Institute of Chemistry and Chemical Technology, Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia.

Macromolecule Content 

  • Total Structure Weight: 30.17 kDa 
  • Atom Count: 2,419 
  • Modeled Residue Count: 258 
  • Deposited Residue Count: 260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2A [auth AAA]260Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.170 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.145 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.555α = 90
b = 41.636β = 104.467
c = 72.519γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Database references