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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acidic mammalian chitinase
A, B
395Homo sapiensMutation(s): 4 
Gene Names: CHIA
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RM8
Query on RM8

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-methyl-3-{[4-(pyridin-2-yl)piperazin-1-yl]methyl}-1H-indole
C19 H22 N4
ZAXKSLQZANTESC-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RM8 BindingDB:  3RM8 IC50: 700 (nM) from 1 assay(s)
PDBBind:  3RM8 IC50: 700 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment 


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
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description