AMCase in complex with Compound 5

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report

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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: https://doi.org/10.1021/jm100533p
  • Primary Citation of Related Structures:  
    3RM4, 3RM8, 3RM9, 3RME

  • PubMed Abstract: 

    Acidic mammalian chitinase (AMCase) is a member of the glycosyl hydrolase 18 family (EC 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acidic mammalian chitinase
A, B
395Homo sapiensMutation(s): 4 
Gene Names: CHIA
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZP6 (Homo sapiens)
Explore Q9BZP6 
Go to UniProtKB:  Q9BZP6
GTEx:  ENSG00000134216 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZP6
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
RME BindingDB:  3RME IC50: 2.20e+4 (nM) from 1 assay(s)
PDBBind:  3RME IC50: 2.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.558α = 90
b = 89.482β = 90
c = 126.48γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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