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: 29612.79 
• Atom Count: 2090 
• Residue Count: 260 
• Unique protein chains: 1

3DD0

Use of Carbonic Anhydrase II, IX Active-Site Mimic, for the Purpose of Screening Inhibitors for Possible Anti-Cancer Properties

• DOI: 10.2210/pdb3DD0/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2008-06-04 Released: 2009-03-03 
• Deposition Author(s): Genis, C., Sippel, K.H., Case, N., Govindasamy, L., Agbandje-Mckenna, M., Mckenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.180 
• R-Value Work: 0.149 

Literature

Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties

Genis, C., Sippel, K.H., Case, N., Cao, W., Avvaru, B.S., Tartaglia, L.J., Govindasamy, L., Tu, C., Agbandje-McKenna, M., Silverman, D.N., Rosser, C.J., McKenna, R.

(2009) Biochemistry 48: 1322-1331

• PubMed: 19170619 
• DOI: 10.1021/bi802035f
• Primary Citation of Related Structures:  
  3DCW, 3DCS, 3DCC, 3DC9, 3DC3, 3DBU, 3DAZ, 3D9Z, 3D8W
• Also Cited By: 3OKV, 3OKU, 3OIM, 3OIL, 3OIK


• PubMed Abstract: 
  

Recently, a convincing body of evidence has accumulated suggesting that the overexpression of carbonic anhydrase isozyme IX (CA IX) in some cancers contributes to the acidification of the extracellular matrix, which in turn promotes the growth and metastasis of the tumor. These observations have made CA IX an attractive drug target for the selective treatment of certain cancers. Currently, there is no available X-ray crystal structure of CA IX, and this lack of availability has hampered the rational design of selective CA IX inhibitors. In light of these observations and on the basis of structural alignment homology, using the crystal structure of carbonic anhydrase II (CA II) and the sequence of CA IX, a double mutant of CA II with Ala65 replaced by Ser and Asn67 replaced by Gln has been constructed to resemble the active site of CA IX. This CA IX mimic has been characterized kinetically using (18)O-exchange and structurally using X-ray crystallography, alone and in complex with five CA sulfonamide-based inhibitors (acetazolamide, benzolamide, chlorzolamide, ethoxzolamide, and methazolamide), and compared to CA II. This structural information has been evaluated by both inhibition studies and in vitro cytotoxicity assays and shows a correlated structure-activity relationship. Kinetic and structural studies of CA II and CA IX mimic reveal chlorzolamide to be a more potent inhibitor of CA IX, inducing an active-site conformational change upon binding. Additionally, chlorzolamide appears to be cytotoxic to prostate cancer cells. This preliminary study demonstrates that the CA IX mimic may provide a useful model to design more isozyme-specific CA IX inhibitors, which may lead to development of new therapeutic treatments of some cancers.

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Organizational Affiliation: 

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

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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EZL	IC50: 0.3 - 3 nM (100) BINDINGDB
EZL	Kd: 0.7 - 1.1 nM (100) BINDINGDB
EZL	Ki: <1 - 8000 nM (100) BINDINGDB
EZL	Ki: <1 nM BINDINGMOAD
EZL	Ki: 1 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.180 
• R-Value Work: 0.149 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.820	α = 90.00
b = 41.680	β = 104.56
c = 72.850	γ = 90.00

Software Package:

Software Name	Purpose
SHELXL-97	refinement
HKL-2000	data reduction
SHELX	phasing
CrystalClear	data collection
HKL-2000	data scaling
SHELX	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-04 
• Released Date: 2009-03-03 
• Deposition Author(s): Genis, C., Sippel, K.H., Case, N., Govindasamy, L., Agbandje-Mckenna, M., Mckenna, R.

Revision History 

• Version 1.0: 2009-03-03
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance