Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30062.04 
• Atom Count: 2122 
• Residue Count: 260 
• Unique protein chains: 1

3CAJ

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

• DOI: 10.2210/pdb3CAJ/pdb

• Classification: LYASE
• Organism(s): Homo sapiens


• Deposited: 2008-02-20 Released: 2008-04-08 
• Deposition Author(s): Di Fiore, A., De Simone, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.214 
• R-Value Work: 0.180 

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

• PubMed: 18359629 
• DOI: 10.1016/j.bmcl.2008.03.023


• 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. 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.

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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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MBO	A	MERCURIBENZOIC ACID C7 H5 Hg O2 FVFZSVRSDNUCGG-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EZL	A	6-ethoxy-1,3-benzothiazole-2-sulfonamide Ethoxzolamide C9 H10 N2 O3 S2 OUZWUKMCLIBBOG-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EZL	Ki: 0.5 - 320 nM (100) BINDINGDB
EZL	Kd: 0.7 - 1.1 nM (100) BINDINGDB
EZL	IC50: 0.3 - 3 nM (100) BINDINGDB
CL	Ki: 200000000 nM (100) BINDINGDB
EZL	Ki: 8 nM BINDINGMOAD
EZL	Ki: 8 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.214 
• R-Value Work: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.210	α = 90.00
b = 41.360	β = 104.35
c = 72.030	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	phasing
SCALEPACK	data scaling
MAR345	data collection
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-20 
• Released Date: 2008-04-08 
• Deposition Author(s): Di Fiore, A., De Simone, G.

Revision History 

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