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
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XNF (Subject of Investigation/LOI)
Query on XNF

Download Ideal Coordinates CCD File 
E [auth AAA]4-[[(~{S})-dimethoxyphosphoryl-[4-[(~{S})-dimethoxyphosphoryl-[(4-sulfamoylphenyl)amino]methyl]phenyl]methyl]amino]benzenesulfonamide
C24 H32 N4 O10 P2 S2
WAFYATGDBDLIRD-PSWAGMNNSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth AAA]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth AAA]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth AAA]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
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

View Full Validation Report



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