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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/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 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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptase beta 2
A, B, C, D
245Homo sapiensMutation(s): 0 
EC: 3.4.21.59
UniProt & NIH Common Fund Data Resources
Find proteins for P20231 (Homo sapiens)
Explore P20231 
Go to UniProtKB:  P20231
PHAROS:  P20231
GTEx:  ENSG00000197253 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20231
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
2FF PDBBind:  2ZA5 Ki: 3.7 (nM) from 1 assay(s)
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary