2EU2 | pdb_00002eu2

Human Carbonic Anhydrase II in complex with novel inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2EU2/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-10-28 Released: 2006-07-11 
• Deposition Author(s): Fisher, S.Z., Govindasamy, L., Boyle, N., Agbandje-McKenna, M., Silverman, D.N., Blackburn, G.M., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.166 (Depositor), 0.138 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

X-ray crystallographic studies reveal that the incorporation of spacer groups in carbonic anhydrase inhibitors causes alternate binding modes.

Fisher, S.Z., Govindasamy, L., Boyle, N., Agbandje-McKenna, M., Silverman, D.N., Blackburn, G.M., McKenna, R.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 618-622

• PubMed: 16820676 
• DOI: https://doi.org/10.1107/S1744309106020446
• Primary Citation Related Structures: 
  2EU2, 2EU3


• PubMed Abstract: 
  

  Human carbonic anhydrases (CAs) are well studied targets for the development of inhibitors for pharmaceutical applications. The crystal structure of human CA II has been determined in complex with two CA inhibitors (CAIs) containing conventional sulfonamide and thiadiazole moieties separated by a -CF2- or -CHNH2- spacer group. The structures presented here reveal that these spacer groups allow novel binding modes for the thiadiazole moiety compared with conventional CAIs.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.59 kDa 
• Atom Count: 2,384 
• Modeled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5DS	C [auth A]	(R)-1-AMINO-1-[5-(DIMETHYLAMINO)-1,3,4-THIADIAZOL-2-YL]METHANESULFONAMIDE C5 H11 N5 O2 S2 PBUMATDKSRINDG-GSVOUGTGSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.166 (Depositor), 0.138 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.965	α = 90
b = 42.057	β = 104.03
c = 72.412	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-11 
Deposition Author(s): Fisher, S.Z., Govindasamy, L., Boyle, N., Agbandje-McKenna, M., Silverman, D.N., Blackburn, G.M., McKenna, R.

Revision History  

• Version 1.0: 2006-07-11
  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: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2019-08-14
  Changes: Data collection
• Version 1.6: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description