3RME

AMCase in complex with Compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification and Characterization of Acidic Mammalian Chitinase Inhibitors

Cole, D.C.Olland, A.M.Jacob, J.Brooks, J.Bursavich, M.G.Czerwinski, R.Declercq, C.Johnson, M.Joseph-McCarthy, D.Ellingboe, J.W.Lin, L.Nowak, P.Presman, E.Strand, J.Tam, A.Williams, C.M.M.Yao, S.Tsao, D.H.H.Fitz, L.J.

(2010) J.Med.Chem. 53: 6122-6128

  • DOI: 10.1021/jm100533p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acidic mammalian chitinase (AMCase) is a member of the glycosyl hydrolase 18 family (EC 3.2.1.14) that has been implicated in the pathophysiology of allergic airway disease such as asthma. Small molecule inhibitors of AMCase were identified using a c ...

    Acidic mammalian chitinase (AMCase) is a member of the glycosyl hydrolase 18 family (EC 3.2.1.14) that has been implicated in the pathophysiology of allergic airway disease such as asthma. Small molecule inhibitors of AMCase were identified using a combination of high-throughput screening, fragment screening, and virtual screening techniques and characterized by enzyme inhibition and NMR and Biacore binding experiments. X-ray structures of the inhibitors in complex with AMCase revealed that the larger more potent HTS hits, e.g. 5-(4-(2-(4-bromophenoxy)ethyl)piperazine-1-yl)-1H-1,2,4-triazol-3-amine 1, spanned from the active site pocket to a hydrophobic pocket. Smaller fragments identified by FBS occupy both these pockets independently and suggest potential strategies for linking fragments. Compound 1 is a 200 nM AMCase inhibitor which reduced AMCase enzymatic activity in the bronchoalveolar lavage fluid in allergen-challenged mice after oral dosing.


    Organizational Affiliation

    WorldWide Medicinal Chemistry: Inflammation & Immunology, Pfizer Global Research & Development, Cambridge, MA 01240, USA. derek.cole@takedasd.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acidic mammalian chitinase
A, B
395Homo sapiensMutation(s): 0 
Gene Names: CHIA
EC: 3.2.1.14
Find proteins for Q9BZP6 (Homo sapiens)
Go to Gene View: CHIA
Go to UniProtKB:  Q9BZP6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RME
Query on RME

Download SDF File 
Download CCD File 
A, B
N-ethyl-2-(4-methylpiperazin-1-yl)pyridine-3-carboxamide
C13 H20 N4 O
KCRYVRIFQJRTDD-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RMEIC50: 22000 nM (98) BINDINGDB
RMEIC50: 22000 nM BINDINGMOAD
RMEIC50: 22000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.558α = 90.00
b = 89.482β = 90.00
c = 126.480γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-04-20 
  • Released Date: 2011-08-24 
  • Deposition Author(s): Olland, A.

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release