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 

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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 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MBO
Query on MBO
Download Ideal Coordinates CCD File 
E [auth A]MERCURIBENZOIC ACID
C7 H5 Hg O2
FVFZSVRSDNUCGG-UHFFFAOYSA-N		 Ligand Interaction
EZL
Query on EZL
Download Ideal Coordinates CCD File 
D [auth A]6-ethoxy-1,3-benzothiazole-2-sulfonamide
C9 H10 N2 O3 S2
OUZWUKMCLIBBOG-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CL BindingDB:  3CAJ Ki: min: 2.00e+8, max: 2.00e+8 (nM) from 2 assay(s)
EZL BindingDB:  3CAJ Ki: min: 0.49, max: 320 (nM) from 6 assay(s)
Kd: min: 0.71, max: 1.1 (nM) from 2 assay(s)
IC50: min: 0.3, max: 3 (nM) from 2 assay(s)
Binding MOAD:  3CAJ Ki: 8 (nM) from 1 assay(s)
PDBBind:  3CAJ Ki: 8 (nM) from 1 assay(s)
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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