Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.94 kDa 
• Atom Count: 2145 
• Residue Count: 256 
• Unique protein chains: 1

1CNW

SECONDARY INTERACTIONS SIGNIFICANTLY REMOVED FROM THE SULFONAMIDE BINDING POCKET OF CARBONIC ANHYDRASE II INFLUENCE BINDING CONSTANTS

• DOI: 10.2210/pdb1CNW/pdb

• Classification: LYASE (OXO-ACID)
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1995-07-21 Released: 1995-11-14 
• Deposition Author(s): Boriack, P.A., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.174 

Literature

Secondary interactions significantly removed from the sulfonamide binding pocket of carbonic anhydrase II influence inhibitor binding constants.

Boriack, P.A., Christianson, D.W., Kingery-Wood, J., Whitesides, G.M.

(1995) J Med Chem 38: 2286-2291

• PubMed: 7608893 
• DOI: 10.1021/jm00013a004
• Primary Citation of Related Structures:  
  1CNY, 1CNX, 1CNW


• PubMed Abstract: 
  

A series of competitive inhibitors of carbonic anhydrase II (CAII; EC 4.2.1.1) that consists of oligo(ethylene glycol) units attached to p-benzenesulfonamides with pendant amino acids, H2NSO2C6H4CONHCH2CH2OCH2CH2OCH2CH2NHCOCHRNH3+, have been synthesized and examined using competitive fluorescence assays. Three of the strongest inhibitors, designated EG3NH3+, EG3GlyNH3+, and EG3PheNH3+, have been studied by X-ray crystallographic methods at limiting resolutions of 1.9, 2.0, and 2.3 A, respectively. The sulfonamide-zinc binding modes and the association of the ethylene glycol linkers to the hydrophobic patch of the active site are similar in all three inhibitors. Differences in the values of Kd are therefore not due to differences in zinc coordination or to differences in the modes of enzyme-glycol association but instead appear to arise from interaction of the pendant amino acids with the surface of the protein. These pendant groups are, however, not sufficiently ordered to be visible in electron density maps. Thus, structural variations of inhibitors at locations distant from the primary binding (i.e., the sulfonamide group) site affect the overall binding affinities of inhibitors (e.g., Kd (EG3PheNH3+) = 14 nM as compared with Kd (EG3GluNH3+) = 100 nM).

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Organizational Affiliation: 

Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE II	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EG1	A	AMINOMETHYLENECARBONYLAMINODI(ETHYLOXY)ETHYLAMINOCARBONYLBENZENESULFONAMIDE C15 H24 N4 O6 S OIKKGRHOXPAPMW-UHFFFAOYSA-N
HG	A	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
EG1	Kd:  19   nM  Binding MOAD
EG1	Kd :  19   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.7	α = 90
b = 41.7	β = 104.6
c = 73	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-07-21 
• Released Date: 1995-11-14 
Deposition Author(s): Boriack, P.A., Christianson, D.W.

Revision History 

• Version 1.0: 1995-11-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance