6B59

Carbonic anhydrase II in complex with nitrogenous base-bearing benezenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

wwPDB Validation 3D Report Full Report



Literature

Discovery of New Sulfonamide Carbonic Anhydrase IX Inhibitors Incorporating Nitrogenous Bases.

Nocentini, A.Bua, S.Lomelino, C.L.McKenna, R.Menicatti, M.Bartolucci, G.Tenci, B.Di Cesare Mannelli, L.Ghelardini, C.Gratteri, P.Supuran, C.T.

(2017) ACS Med Chem Lett 8: 1314-1319

  • DOI: 10.1021/acsmedchemlett.7b00399
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Incorporation of the purine/pyrimidine moieties as tails to classical benzenesulfonamide scaffolds afforded two series of human (h) carbonic anhydrase (CA, EC 4.2.1.1) inhibitors. The compounds were designed according to the molecular hybridization a ...

    Incorporation of the purine/pyrimidine moieties as tails to classical benzenesulfonamide scaffolds afforded two series of human (h) carbonic anhydrase (CA, EC 4.2.1.1) inhibitors. The compounds were designed according to the molecular hybridization approach, in order to modulate the interaction with different CA isozymes and exploit the antitumor effect of uracil and adenine derivatives in parallel and synergic mode to the inhibition of the tumor-associated hCA IX. The sulfonamides were investigated as inhibitors of four isoforms, cytosolic hCA I/II and transmembrane hCA IV/IX. The inhibitory profiles were dependent on the length and positioning of the spacer connecting the two pharmacophores. X-ray crystallography demonstrated the binding mode of an inhibitor to hCA II and hCA IX-mimic. Compounds endowed with the best hCA IX inhibitory efficacy were evaluated for antiproliferative activity against HT-29 colon cancer cell lines. The in vitro results suggest multiple mechanisms of action are responsible for the compounds' cytotoxic efficacy.


    Organizational Affiliation

    Department of NEUROFARBA, Pharmaceutical and Nutraceutical section, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
257Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CQS
Query on CQS

Download CCD File 
A
2-(6-amino-9H-purin-9-yl)-N-[2-(4-sulfamoylphenyl)ethyl]acetamide
C15 H17 N7 O3 S
PUMWMJFQZZVYPO-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CQSKi:  8.199999809265137   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.646α = 90
b = 41.667β = 104.18
c = 72.633γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release