3RM4

AMCase in complex with Compound 1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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:  
    3RME, 3RM8, 3RM9, 3RM4

  • 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 combination of high-throughput screening, fragment screening, and virtual screening techniques and characterized by enzyme inhibition and NMR and Biacore binding experiments ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acidic mammalian chitinase A, 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
GTEx:  ENSG00000134216
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3RM
Query on 3RM
Download Ideal Coordinates CCD File 
A, B
5-{4-[2-(4-bromophenoxy)ethyl]piperazin-1-yl}-4H-1,2,4-triazol-3-amine
C14 H19 Br N6 O
GGFPYJPCWQIIKE-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3RMKd :  1690   nM  PDBBind
3RMIC50:  210   nM  BindingDB
3RMIC50:  210   nM  Binding MOAD
3RMIC50:  5450   nM  BindingDB
3RMKd:  1690   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.498α = 90
b = 89.371β = 90
c = 126.991γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-04-20 
  • 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