Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | 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: 29.22 kDa 
• Atom Count: 2207 
• Modelled Residue Count: 257 
• Deposited Residue Count: 257 
• Unique protein chains: 1

4G0C

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

• PDB DOI: 10.2210/pdb4G0C/pdb

• Classification: LYASE/LYASE inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.00 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
• Primary Citation of Related Structures:  
  4G0C


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	257	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZM	C [auth A]	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C4 H6 N4 O3 S2 BZKPWHYZMXOIDC-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AZM	BindingDB:  4G0C	Ki: min: 0.01, max: 104 (nM) from 25 assay(s)
		Kd: min: 0.06, max: 46 (nM) from 12 assay(s)
		IC50: min: 0.49, max: 4500 (nM) from 61 assay(s)
	PDBBind:  4G0C	Ki: 12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.283 
• R-Value Work: 0.267 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.84	α = 90
b = 41.76	β = 104.31
c = 72.94	γ = 90

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description, Structure summary
• Version 1.3: 2018-04-25
  Changes: Data collection