Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 30.06 kDa 
• Atom Count: 2425 
• Residue Count: 258 
• 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
• Mutation(s): No 


• 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: 1.80 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
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(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 GTEx  ENSG00000104267

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBO	A	MERCURIBENZOIC ACID C7 H5 Hg O2 FVFZSVRSDNUCGG-UHFFFAOYSA-N
EZL	A	6-ethoxy-1,3-benzothiazole-2-sulfonamide C9 H10 N2 O3 S2 OUZWUKMCLIBBOG-UHFFFAOYSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EZL	Ki:  38   nM  BindingDB
EZL	Ki:  8   nM  BindingDB
EZL	IC50:  0.30000001192092896   nM  BindingDB
CL	Ki:  200000000   nM  BindingDB
EZL	Ki:  8   nM  Binding MOAD
EZL	Ki:  320   nM  BindingDB
EZL	Kd:  0.7099999785423279   nM  BindingDB
EZL	Ki:  0.49000000953674316   nM  BindingDB
EZL	IC50:  3   nM  BindingDB
CL	Ki:  200000000   nM  BindingDB
EZL	Kd:  1.100000023841858   nM  BindingDB
EZL	Ki:  5.400000095367432   nM  BindingDB
EZL	Ki :  8   nM  PDBBind
EZL	Ki:  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 = 42.21	α = 90
b = 41.36	β = 104.35
c = 72.03	γ = 90

Software Package:

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

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
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description