3CAJ

Crystal structure of the human carbonic anhydrase II in complex with ethoxzolamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Carbonic anhydrase inhibitors: the X-ray crystal structure of ethoxzolamide complexed to human isoform II reveals the importance of thr200 and gln92 for obtaining tight-binding inhibitors

Di Fiore, A.Pedone, C.Antel, J.Waldeck, H.Witte, A.Wurl, M.Scozzafava, A.Supuran, C.T.De Simone, G.

(2008) Bioorg Med Chem Lett 18: 2669-2674

  • DOI: 10.1016/j.bmcl.2008.03.023
  • Primary Citation of Related Structures:  
    3CAJ

  • PubMed Abstract: 
  • Ethoxzolamide, an almost forgotten inhibitor of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1), is the only classical inhibitor whose structure in adduct with any isoform was not reported yet. We report here the inhibition data of this molecul ...

    Ethoxzolamide, an almost forgotten inhibitor of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1), is the only classical inhibitor whose structure in adduct with any isoform was not reported yet. We report here the inhibition data of this molecule with the 12 catalytically active mammalian isozymes (CA I-CA XIV) and the X-ray crystal structure with the cytosolic, ubiquitous isoform CA II. These data are presumably useful for the design of novel CA inhibitors, targeting various CA isozymes, considering that ethoxzolamide was already the lead molecule to obtain the second generation inhibitors, dorzolamide and brinzolamide, clinically used antiglaucoma agents with topical action, as well as various other investigational agents.


    Related Citations: 
    • Positions of His-64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors
      Smith, G.M., Alexander, R.S., Christianson, D.W., McKeever, B.M., Ponticello, G.S., Springer, J.P., Randall, W.C., Baldwin, J.J., Habecker, C.N.
      (1994) Protein Sci 3: 118
    • Structures of murine carbonic anhydrase IV and human carbonic anhydrase II complexed with brinzolamide: molecular basis of isozyme-drug discrimination
      Stams, T., Chen, Y., Boriack-Sjodin, P.A., Hurt, J.D., Liao, J., May, J.A., Dean, T., Laipis, P., Silverman, D.N., Christianson, D.W.
      (1998) Protein Sci 7: 556

    Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MBO
Query on MBO

Download CCD File 
A
MERCURIBENZOIC ACID
C7 H5 Hg O2
FVFZSVRSDNUCGG-UHFFFAOYSA-N
 Ligand Interaction
EZL
Query on EZL

Download CCD File 
A
6-ethoxy-1,3-benzothiazole-2-sulfonamide
C9 H10 N2 O3 S2
OUZWUKMCLIBBOG-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EZLKi:  38   nM  BindingDB
EZLKi:  8   nM  BindingDB
EZLIC50:  0.30000001192092896   nM  BindingDB
CLKi:  200000000   nM  BindingDB
EZLKi:  8   nM  Binding MOAD
EZLKi:  320   nM  BindingDB
EZLKd:  0.7099999785423279   nM  BindingDB
EZLKi:  0.49000000953674316   nM  BindingDB
EZLIC50:  3   nM  BindingDB
CLKi:  200000000   nM  BindingDB
EZLKd:  1.100000023841858   nM  BindingDB
EZLKi:  5.400000095367432   nM  BindingDB
EZLKi :  8   nM  PDBBind
EZLKi:  1   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.21α = 90
b = 41.36β = 104.35
c = 72.03γ = 90
Software Package:
Software NamePurpose
MAR345data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description