2FS8

Human beta-tryptase II with inhibitor CRA-29382


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1021/bi060173m
  • Primary Citation of Related Structures:  
    2FPZ, 2FS9, 2FS8, 2FWW, 2FX6, 2FX4, 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 ...

    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



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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C3A
Query on C3A

Download CCD File 
A, B, C, D
ALLYL {(1S)-1-[(5-{4-[(2,3-DIHYDRO-1H-INDEN-2-YLAMINO)CARBONYL]BENZYL}-1,2,4-OXADIAZOL-3-YL)CARBONYL]-3-PYRROLIDIN-3-YLPROPYL}CARBAMATE
C31 H35 N5 O5
YCRRSNQAJBEKFO-QFQXNSOFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C3AKi :  25   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.210 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.202α = 90
b = 78.202β = 90
c = 165.516γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-01-21 
  • Released Date: 2006-03-21 
  • Deposition Author(s): Somoza, J.R.

Revision History 

  • Version 1.0: 2006-03-21
    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