3RM8

AMCase in complex with Compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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 chitinaseA, B395Homo sapiensMutation(s): 4 
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RM8
Query on RM8

Download CCD File 
A, B
2-methyl-3-{[4-(pyridin-2-yl)piperazin-1-yl]methyl}-1H-indole
C19 H22 N4
ZAXKSLQZANTESC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RM8IC50 :  700   nM  PDBBind
RM8IC50:  700   nM  BindingDB
RM8IC50:  700   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.684α = 90
b = 89.248β = 90
c = 125.804γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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