3R17

hCarbonic anhydrase II bound to N-(2-fluoro.4-sulfamoylphenyl)-2-(thiophen-2-yl) acetamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Conformational variability of different sulfonamide inhibitors with thienyl-acetamido moieties attributes to differential binding in the active site of cytosolic human carbonic anhydrase isoforms.

Biswas, S., Aggarwal, M., Guzel, O., Scozzafava, A., McKenna, R., Supuran, C.T.

(2011) Bioorg.Med.Chem. 19: 3732-3738

  • DOI: 10.1016/j.bmc.2011.05.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The X-ray crystal structures of the adducts of human carbonic anhydrase (hCA, EC 4.2.1.1) II complexed with two aromatic sulfonamides incorporating 2-thienylacetamido moieties are reported here. Although, the two inhibitors only differ by the presenc ...

    The X-ray crystal structures of the adducts of human carbonic anhydrase (hCA, EC 4.2.1.1) II complexed with two aromatic sulfonamides incorporating 2-thienylacetamido moieties are reported here. Although, the two inhibitors only differ by the presence of an additional 3-fluoro substituent on the 4-amino-benzenesulfonamide scaffold, their inhibition profiles against the cytosolic isoforms hCA I, II, III, VII and XIII are quite different. These differences were rationalized based on the obtained X-ray crystal structures, and their comparison with other sulfonamide CA inhibitors with clinical applications, such as acetazolamide, methazolamide and dichlorophenamide. The conformations of the 2-thienylacetamido tails in the hCA II adducts of the two sulfonamides were highly different, although the benzenesulfonamide parts were superimposable. Specific interactions between structurally different inhibitors and amino acid residues present only in some considered isoforms have thus been evidenced. These findings can explain the high affinity of the 2-thienylacetamido benzenesulfonamides for some pharmacologically relevant CAs (i.e., isoforms II and VII) being also useful to design high affinity, more selective sulfonamide inhibitors of various CAs.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
B
257Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5UM
Query on 5UM
Download SDF File 
Download CCD File 
B
N-(2-fluoro-4-sulfamoylphenyl)-2-(thiophen-2-yl)acetamide
C12 H11 F N2 O3 S2
XAKMDYVUOKFDSL-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS
Download SDF File 
Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5UMKi: 390 nM (100) BINDINGDB
5UMKi: 390 nM BINDINGMOAD
5UMKi: 390 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.378α = 90.00
b = 41.261β = 104.17
c = 71.943γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance