2YBT

Crystal structure of human acidic chitinase in complex with bisdionin C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Analyzing airway inflammation with chemical biology: dissection of acidic mammalian chitinase function with a selective drug-like inhibitor.

Sutherland, T.E.Andersen, O.A.Betou, M.Eggleston, I.M.Maizels, R.M.van Aalten, D.Allen, J.E.

(2011) Chem Biol 18: 569-579

  • DOI: 10.1016/j.chembiol.2011.02.017
  • Primary Citation of Related Structures:  
    2YBT, 2YBU

  • PubMed Abstract: 
  • Acidic mammalian chitinase (AMCase) is produced in the lung during allergic inflammation and asthma, and inhibition of enzymatic activity has been considered as a therapeutic strategy. However, most chitinase inhibitors are nonselective, additionally inhibiting chitotriosidase activity ...

    Acidic mammalian chitinase (AMCase) is produced in the lung during allergic inflammation and asthma, and inhibition of enzymatic activity has been considered as a therapeutic strategy. However, most chitinase inhibitors are nonselective, additionally inhibiting chitotriosidase activity. Here, we describe bisdionin F, a competitive AMCase inhibitor with 20-fold selectivity for AMCase over chitotriosidase, designed by utilizing the AMCase crystal structure and dicaffeine scaffold. In a murine model of allergic inflammation, bisdionin F-treatment attenuated chitinase activity and alleviated the primary features of allergic inflammation including eosinophilia. However, selective AMCase inhibition by bisdionin F also caused dramatic and unexpected neutrophilia in the lungs. This class of inhibitor will be a powerful tool to dissect the functions of mammalian chitinases in disease and represents a synthetically accessible scaffold to optimize inhibitory properties in terms of airway inflammation.


    Organizational Affiliation

    Centre for Immunity, Infection and Evolution, and the Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Scotland, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACIDIC MAMMALIAN CHITINASEA, B, C, D, E, F381Homo sapiensMutation(s): 3 
Gene Names: CHIA
EC: 3.2.1.14
Find proteins for Q9BZP6 (Homo sapiens)
Explore Q9BZP6 
Go to UniProtKB:  Q9BZP6
NIH Common Fund Data Resources
PHAROS:  Q9BZP6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DW0
Query on DW0

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , K [auth B] , L [auth B] , N [auth C] , O [auth C] , Q [auth D] , R [auth D] , 
H [auth A],  I [auth A],  K [auth B],  L [auth B],  N [auth C],  O [auth C],  Q [auth D],  R [auth D],  T [auth E],  U [auth E],  W [auth F],  X [auth F]
1,1'-PROPANE-1,3-DIYLBIS(3,7-DIMETHYL-3,7-DIHYDRO-1H-PURINE-2,6-DIONE)
C17 H20 N8 O4
KEPIKAFUZRKZMT-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DW0IC50:  20000   nM  Binding MOAD
DW0IC50 :  20000   nM  PDBBind
DW0IC50:  20000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.207α = 90
b = 149.066β = 90
c = 152.082γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-02-14
    Changes: Database references