2YBU | pdb_00002ybu

Crystal structure of human acidic chitinase in complex with bisdionin F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.219 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2YBU

Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.chembiol.2011.02.017
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 260.95 kDa 
  • Atom Count: 19,347 
  • Modeled Residue Count: 2,256 
  • Deposited Residue Count: 2,286 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACIDIC MAMMALIAN CHITINASE
A, B, C, D, E
A, B, C, D, E, F
381Homo sapiensMutation(s): 3 
EC: 3.2.1.14
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZP6 (Homo sapiens)
Explore Q9BZP6 
Go to UniProtKB:  Q9BZP6
PHAROS:  Q9BZP6
GTEx:  ENSG00000134216 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZP6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CX9

Query on CX9



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
K [auth B]
L [auth B]
N [auth C]
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]
3,7-DIMETHYL-1-[3-(3-METHYL-2,6-DIOXO-9H-PURIN-1-YL)PROPYL]PURINE-2,6-DIONE
C16 H18 N8 O4
PUHJHZQYIBJCSQ-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
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
Binding Affinity Annotations 
IDSourceBinding Affinity
CX9 BindingDB:  2YBU Ki: 260 (nM) from 1 assay(s)
IC50: 920 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.219 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.781α = 90
b = 149.194β = 90
c = 151.278γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary