2FS9

Human beta tryptase II with inhibitor CRA-28427


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 

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:  

  • 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 inhibi ...

    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: 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
C4A
Query on C4A

Download SDF File 
Download CCD File 
A, B, C, D
ETHYL {(1S)-5-AMINO-1-[(5-{4-[(2,3-DIHYDRO-1H-INDEN-2-YLAMINO)CARBONYL]BENZYL}-1,2,4-OXADIAZOL-3-YL)CARBONYL]PENTYL}CARBAMATE
C28 H33 N5 O5
PWHBUXLKTXHYAP-QHCPKHFHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C4AKi: 2.8 - 3 nM (99) BINDINGDB
C4AKi: 3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 78.055α = 90.00
b = 78.055β = 90.00
c = 164.424γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-01-21 
  • Released Date: 2006-03-07 
  • Deposition Author(s): Somoza, J.R.

Revision History 

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description