2ZA5

Crystal Structure of human tryptase with potent non-peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Potent, nonpeptide inhibitors of human mast cell tryptase. Synthesis and biological evaluation of novel spirocyclic piperidine amide derivatives

Costanzo, M.J.Yabut, S.C.Zhang, H.-C.White, K.B.de Garavilla, L.Wang, Y.Minor, L.K.Tounge, B.A.Barnakov, A.N.Lewandowski, F.Milligan, C.Spurlino, J.C.Abraham, W.M.Boswell-Smith, V.Page, C.P.Maryanoff, B.E.

(2008) Bioorg Med Chem Lett 18: 2114-2121

  • DOI: 10.1016/j.bmcl.2008.01.093
  • Primary Citation of Related Structures:  
    2ZA5, 2ZEB, 2ZEC

  • PubMed Abstract: 
  • We have explored a series of spirocyclic piperidine amide derivatives (5) as tryptase inhibitors. Thus, 4 (JNJ-27390467) was identified as a potent, selective tryptase inhibitor with oral efficacy in two animal models of airway inflammation (sheep an ...

    We have explored a series of spirocyclic piperidine amide derivatives (5) as tryptase inhibitors. Thus, 4 (JNJ-27390467) was identified as a potent, selective tryptase inhibitor with oral efficacy in two animal models of airway inflammation (sheep and guinea pig asthma models). An X-ray co-crystal structure of 4 x tryptase revealed a hydrophobic pocket in the enzyme's active site, which is induced by the phenylethynyl group and is comprised of amino acid residues from two different monomers of the tetrameric protein.


    Related Citations: 
    • Potent, small-molecule inhibitors of human mast cell tryptase. Antiasthmatic action of a dipeptide-based transition-state analogue containing a benzothiazole ketone
      Costanzo, M.J., Yabut, S.C., Almond, H.R., Andrade-Gordon, P., Corcoran, T.W., de Garavilla, L., Kauffman, J.A., Abraham, W.M., Recacha, R., Chattopadhyay, D., Maryanoff, B.E.
      (2003) J Med Chem 46: 3865

    Organizational Affiliation

    Research and Early Development, Johnson & Johnson Pharmaceutical Research & Development, Welsh & McKean Roads, Spring House, PA 19477-0776, USA. mcostanz@prdus.jnj.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptase beta 2ABCD245Homo sapiensMutation(s): 0 
Gene Names: TPSB2TPS2
EC: 3.4.21.59
Find proteins for P20231 (Homo sapiens)
Explore P20231 
Go to UniProtKB:  P20231
NIH Common Fund Data Resources
PHAROS  P20231
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2FF
Query on 2FF

Download CCD File 
A, B, C, D
(5-(aminomethyl)-2H-spiro[benzofuran-3,4'-piperidine]-1'-yl)(5-(phenylethynyl)furan-2-yl)methanone
C26 H24 N2 O3
YKTUSHSSKIWDRY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2FFKi :  3.700000047683716   nM  PDBBind
2FFIC50:  3.5999999046325684   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.678α = 90
b = 82.678β = 90
c = 170.284γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description