Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.89 kDa 
• Atom Count: 2245 
• Residue Count: 256 
• Unique protein chains: 1

2H15

Carbonic anhydrase inhibitors: Clashing with Ala65 as a means of designing isozyme-selective inhibitors that show low affinity for the ubiquitous isozyme II

• DOI: 10.2210/pdb2H15/pdb

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


• Deposited: 2006-05-16 Released: 2007-03-27 
• Deposition Author(s): Winum, J.Y., Temperini, C., Ciattini, S., Scozzafava, A., Supuran, C.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Carbonic anhydrase inhibitors: clash with Ala65 as a means for designing inhibitors with low affinity for the ubiquitous isozyme II, exemplified by the crystal structure of the topiramate sulfamide analogue.

Winum, J.Y., Temperini, C., El Cheikh, K., Innocenti, A., Vullo, D., Ciattini, S., Montero, J.L., Scozzafava, A., Supuran, C.T.

(2006) J Med Chem 49: 7024-7031

• PubMed: 17125255 
• DOI: 10.1021/jm060807n
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The sulfamide analogue of the antiepileptic drug topiramate is a 210 times less potent inhibitor of isozyme II of the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1) compared to topiramate but effectively inhibits isozymes CA VA, VB, VII, XIII, and XIV (KI in the range of 21-35 nM). Its weak binding to CA II is due to a clash between one methyl group of the inhibitor and Ala65 and may be exploited for the drug design of compounds with lower affinity for this ubiquitous isozyme, as Ala65 is unique to CA II. As shown by X-ray crystallography, the sulfamide analogue binds to CA II with the deprotonated sulfamide moiety coordinated to Zn(II) and with the organic scaffold making an extended network of hydrogen bonds with Thr199, Gln92, His94, Asn62, and Thr200. Its binding to this isozyme is more similar to that of topiramate and quite different from that of the topiramate cyclic sulfate analogue RWJ-37947.

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Organizational Affiliation: 

Laboratoire de Chimie Biomoléculaire, UMR 5032, Ecole Nationale Supérieure de Chimie de Montpellier, Université Montpellier II, 8 Rue de l'Ecole Normale, 34296 Montpellier Cedex, France.

Macromolecules

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 UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918 GTEx  ENSG00000104267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B19	A	N-{[(3AS,5AR,8AR,8BS)-2,2,7,7-TETRAMETHYLTETRAHYDRO-3AH-BIS[1,3]DIOXOLO[4,5-B:4',5'-D]PYRAN-3A-YL]METHYL}SULFAMIDE C12 H22 N2 O7 S NQRKKQKMTGLNOZ-XBWDGYHZSA-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 %)
B19	Ki:  340000   nM  BindingDB
B19	Ki:  650000   nM  BindingDB
B19	Kd:  25000   nM  BindingDB
B19	Ki :  2135   nM  PDBBind
B19	Ki:  2135   nM  BindingDB
B19	Ki:  2135   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.15	α = 90
b = 41.55	β = 104.23
c = 72.25	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-16 
• Released Date: 2007-03-27 
Deposition Author(s): Winum, J.Y., Temperini, C., Ciattini, S., Scozzafava, A., Supuran, C.T.

Revision History 

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection