human beta-tryptase II complexed with 4-piperidinebutyrate to make acylenzyme

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure-guided design of Peptide-based tryptase inhibitors.

McGrath, M.E.Sprengeler, P.A.Hirschbein, B.Somoza, J.R.Lehoux, I.Janc, J.W.Gjerstad, E.Graupe, M.Estiarte, A.Venkataramani, C.Liu, Y.Yee, R.Ho, J.D.Green, M.J.Lee, C.-S.Liu, L.Tai, V.Spencer, J.Sperandio, D.Katz, B.A.

(2006) Biochemistry 45: 5964-5973

  • DOI: https://doi.org/10.1021/bi060173m
  • Primary Citation of Related Structures:  
    2FPZ, 2FS8, 2FS9, 2FWW, 2FX4, 2FX6, 2FXR

  • PubMed Abstract: 

    Improved peptide-based inhibitors of human beta tryptase were discovered using information gleaned from tripeptide library screening and structure-guided design methods, including fragment screening. Our efforts sought to improve this class of inhibitors by replacing the traditional Lys or Arg P1 element. The optimized compounds display low nanomolar potency against the mast cell target and several hundred-fold selectivity with respect to serine protease off targets. Thus, replacement of Lys/Arg at P1 in a peptide-like scaffold does not need to be accompanied by a loss in target affinity.

  • Organizational Affiliation

    Celera Genomics, Inc., 180 Kimball Way, South San Francisco, California 94080, USA. mary.mcgrath@gilead.com

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 
Gene Names: TPSB2TPS2
UniProt & NIH Common Fund Data Resources
Find proteins for P20231 (Homo sapiens)
Explore P20231 
Go to UniProtKB:  P20231
GTEx:  ENSG00000197253 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20231
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.92α = 90
b = 77.92β = 90
c = 164.03γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2006-02-14 
  • Deposition Author(s): Katz, B.A.

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description