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: 29.60 kDa 
• Atom Count: 2276 
• Residue Count: 258 
• Unique protein chains: 1

1KWR

HUMAN CARBONIC ANHYDRASE II COMPLEXED WITH INHIBITOR 0134-36

• DOI: 10.2210/pdb1KWR/pdb

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


• Deposited: 2002-01-30 Released: 2003-01-07 
• Deposition Author(s): Grueneberg, S., Stubbs, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.269 
• R-Value Work: 0.196 

Literature

Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation.

Gruneberg, S., Stubbs, M.T., Klebe, G.

(2002) J Med Chem 45: 3588-3602

• PubMed: 12166932 
• DOI: 10.1021/jm011112j
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Virtual screening of compound libraries is an alternative and complementary approach to high-throughput screening in the lead discovery process. A new strategy is described to search for possible leads of human carbonic anhydrase II, applying a protocol of several consecutive hierarchical filters involving a preselection based on functional group requirements and fast pharmacophore matching. A suitable pharmacophore is derived by a sophisticated "hot spot" analysis of the binding site to detect regions favorable for protein-ligand interactions. In subsequent steps, molecular similarity with known reference ligands is used to rerank the hits from the pharmacophore matching. Finally the best scored candidates are docked flexibly into the protein binding pocket. After examination of the affinity predictions, 13 compounds were selected for experimental testing. Of these 13, three could be shown to be subnanomolar, one is nanomolar, while a further seven are micromolar inhibitors. The binding mode of two hits could be confirmed by crystal structure analysis. The novelty of the discovered leads is best supported by the fact that a search in the patent literature showed the newly discovered subnanomolar compounds to comprise scaffolds not yet covered by existing patents.

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Related Citations: 

• Subnanomolar Inhibitors from Computer Screening: A Model Study Using Human Carbonic Anhydrase II
  Grueneberg, S., Wendt, B., Klebe, G.
  (2001) Angew Chem Int Ed Engl 40: 389

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Organizational Affiliation: 

Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35032 Marburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbonic anhydrase II	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SG2	A	1-METHYL-3-OXO-1,3-DIHYDRO-BENZO[C]ISOTHIAZOLE-5-SULFONIC ACID AMIDE C8 H8 N2 O3 S2 DFPYCCVFXMWMJM-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SG2	IC50 :  250   nM  PDBBind
SG2	IC50:  250   nM  Binding MOAD
SG2	IC50:  245.5   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.269 
• R-Value Work: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.56	α = 90
b = 41.4	β = 104.4
c = 72.34	γ = 90

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-01-30 
• Released Date: 2003-01-07 
Deposition Author(s): Grueneberg, S., Stubbs, M.T.

Revision History 

• Version 1.0: 2003-01-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance