Biological Assembly 1  

 3D View: Structure | 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: 29220.29 
• Atom Count: 2063 
• Residue Count: 257 
• Unique protein chains: 1

4G0C

Neutron structure of acetazolamide-bound human carbonic anhydrase II reveal molecular details of drug binding.

• DOI: 10.2210/pdb4G0C/pdb

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


• Deposited: 2012-07-09 Released: 2012-09-19 
• Deposition Author(s): Fisher, S.Z., McKenna, R., Aggarwal, M.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.283 
• R-Value Work: 0.267 

Literature

Neutron diffraction of acetazolamide-bound human carbonic anhydrase II reveals atomic details of drug binding.

Fisher, S.Z., Aggarwal, M., Kovalevsky, A.Y., Silverman, D.N., McKenna, R.

(2012) J.Am.Chem.Soc. 134: 14726-14729

• PubMed: 22928733 
• DOI: 10.1021/ja3068098


• PubMed Abstract: 
  

Carbonic anhydrases (CAs) catalyze the hydration of CO(2) forming HCO(3)(-) and a proton, an important reaction for many physiological processes including respiration, fluid secretion, and pH regulation. As such, CA isoforms are prominent clinical targets for treating various diseases. The clinically used acetazolamide (AZM) is a sulfonamide that binds with high affinity to human CA isoform II (HCA II). There are several X-ray structures available of AZM bound to various CA isoforms, but these complexes do not show the charged state of AZM or the hydrogen atom positions of the protein and solvent. Neutron diffraction is a useful technique for directly observing H atoms and the mapping of H-bonding networks that can greatly contribute to rational drug design. To this end, the neutron structure of H/D exchanged HCA II crystals in complex with AZM was determined. The structure reveals the molecular details of AZM binding and the charged state of the bound drug. This represents the first determined neutron structure of a clinically used drug bound to its target.

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Organizational Affiliation: 

Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbonic anhydrase 2	A	257	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
AZM	A	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C4 H6 N4 O3 S2 BZKPWHYZMXOIDC-UHFFFAOYSA-N
DOD	A	DEUTERATED WATER D2 O XLYOFNOQVPJJNP-ZSJDYOACSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AZM	Kd: 6.8 - 46 nM (100) BINDINGDB
AZM	Ki: 0.3 - 3300 nM (100) BINDINGDB
AZM	IC50: 0.5 - 4500 nM (100) BINDINGDB
AZM	Ki: 12 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.283 
• R-Value Work: 0.267 

Software Package:

Software Name	Purpose
PCS	data collection
nCNS	refinement
nCNS	phasing
SCALA	data scaling
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-09 
• Released Date: 2012-09-19 
• Deposition Author(s): Fisher, S.Z., McKenna, R., Aggarwal, M.

Revision History 

• Version 1.0: 2012-09-19
  Type: Initial release
• Version 1.1: 2012-11-21
  Type: Database references
• Version 1.2: 2017-11-15
  Type: Refinement description, Structure summary
• Version 1.3: 2018-04-25
  Type: Data collection