5TUO

Crystal structure of the complex of Helicobacter pylori alpha-carbonic anhydrase with 5-amino-1,3,4-thiadiazole-2-sulfonamide inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report



Literature

Structure-Activity Relationship for Sulfonamide Inhibition of Helicobacter pylori alpha-Carbonic Anhydrase.

Modak, J.K.Liu, Y.C.Supuran, C.T.Roujeinikova, A.

(2016) J Med Chem 59: 11098-11109

  • DOI: 10.1021/acs.jmedchem.6b01333
  • Primary Citation of Related Structures:  
    5TT3, 5TT8, 5TUO, 5TV3

  • PubMed Abstract: 
  • α-Carbonic anhydrase of Helicobacter pylori (HpαCA) plays an important role in the acclimation of this oncobacterium to the acidic pH of the stomach. Sulfonamide inhibitors of HpαCA possess anti-H. pylori activity. The crystal structures of complexes of ...

    α-Carbonic anhydrase of Helicobacter pylori (HpαCA) plays an important role in the acclimation of this oncobacterium to the acidic pH of the stomach. Sulfonamide inhibitors of HpαCA possess anti-H. pylori activity. The crystal structures of complexes of HpαCA with a family of acetazolamide-related sulfonamides have been determined. Analysis of the structures revealed that the mode of sulfonamide binding correlates well with their inhibitory activities. In addition, comparisons with the corresponding inhibitor complexes of human carbonic anhydrase II (HCAII) indicated that HpαCA possesses an additional, alternative binding site for sulfonamides that is not present in HCAII. Furthermore, the hydrophobic pocket in HCAII that stabilizes the apolar moiety of sulfonamide inhibitors is replaced with a more open, hydrophilic pocket in HpαCA. Thus, our analysis identified major structural features can be exploited in the design of selective and more potent inhibitors of HpαCA that may lead to novel antimicrobials.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University , Clayton, Victoria 3800, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-carbonic anhydrase ABCDEFGH234Helicobacter pylori 26695Mutation(s): 0 
Gene Names: C694_06140
EC: 4.2.1.1
Find proteins for A0A0M3KL20 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore A0A0M3KL20 
Go to UniProtKB:  A0A0M3KL20
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1SA
Query on 1SA

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H
5-AMINO-1,3,4-THIADIAZOLE-2-SULFONAMIDE
C2 H4 N4 O2 S2
VGMVBPQOACUDRU-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A, B, C, D, E, G, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1SAKi:  323   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.84α = 90
b = 136.92β = 90.04
c = 166.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHENIXphasing
ADSCdata collection
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release