2ZA5

Crystal Structure of human tryptase with potent non-peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptase beta 2
A, B, C, D
245Homo sapiensMutation(s): 0 
Gene Names: TPSB2 (TPS2)
EC: 3.4.21.59
Find proteins for P20231 (Homo sapiens)
Go to Gene View: TPSB2
Go to UniProtKB:  P20231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2FF
Query on 2FF

Download SDF File 
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 %)
2FFIC50: 3.6 nM BINDINGMOAD
2FFKi: 3.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.181 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 82.678α = 90.00
b = 82.678β = 90.00
c = 170.284γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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