8QUN | pdb_00008qun

human carbonic anhydrase I in complex with 2-((5-cyano-4-hydroxy-6-(p-tolyl)pyrimidin-2-yl)thio)-N-(4-sulfamoylphenyl)acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.215 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.197 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A new framework for novel analogues of pazopanib as potent and selective human carbonic anhydrase inhibitors: Design, repurposing rational, synthesis, crystallographic, in vivo and in vitro biological assessments.

Hefny, S.M.El-Moselhy, T.F.El-Din, N.Ammara, A.Angeli, A.Ferraroni, M.El-Dessouki, A.M.Shaldam, M.A.Yahya, G.Al-Karmalawy, A.A.Supuran, C.T.Tawfik, H.O.

(2024) Eur J Med Chem 274: 116527-116527

  • DOI: https://doi.org/10.1016/j.ejmech.2024.116527
  • Primary Citation of Related Structures:  
    8QUN

  • PubMed Abstract: 

    Herein, we describe the design and synthesis of novel aryl pyrimidine benzenesulfonamides APBSs 5a-n, 6a-c, 7a-b, and 8 as pazopanib analogues to explore new potent and selective inhibitors for the CA IX. All APBSs were examined in vitro for their promising inhibition activity against a small panel of hCAs (isoforms I, II, IX, and XII). The X-ray crystal structure of CA I in adduct with a representative APBS analogue was solved. APBS-5m, endowed with the best hCA IX inhibitory efficacy and selectivity, was evaluated for antiproliferative activity against a small panel of different cancer cell lines, SK-MEL-173, MDA-MB-231, A549, HCT-116, and HeLa, and it demonstrated one-digit IC 50 values range from 2.93 μM (MDA-MB-231) to 5.86 μM (A549). Furthermore, compound APBS-5m was evaluated for its influence on hypoxia-inducible factor (HIF-1α) production, apoptosis induction, and colony formation in MDA-MB-231 cancer cells. The in vivo efficacy of APBS-5m as an antitumor agent was additionally investigated in an animal model of Solid Ehrlich Carcinoma (SEC). In order to offer perceptions into the conveyed hCA IX inhibitory efficacy and selectivity in silico, a molecular docking investigation was also carried out.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt. Electronic address: salma.mosaad@pharm.tanta.edu.eg.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 1A [auth AAA],
B [auth BBB]
261Homo sapiensMutation(s): 0 
Gene Names: CA1
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens)
Explore P00915 
Go to UniProtKB:  P00915
PHAROS:  P00915
GTEx:  ENSG00000133742 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00915
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WZH (Subject of Investigation/LOI)
Query on WZH

Download Ideal Coordinates CCD File 
D [auth AAA],
H [auth BBB]
2-[5-cyano-4-(4-methylphenyl)-6-oxidanyl-pyrimidin-2-yl]sulfanyl-N-(4-sulfamoylphenyl)ethanamide
C20 H17 N5 O4 S2
AIBZOXIWLFUJES-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth BBB]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth AAA],
F [auth BBB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth BBB]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.215 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.197 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.78α = 90
b = 71.39β = 90
c = 121.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata 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: 2024-10-23
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references