2FXR

human beta tryptase II complexed with activated ketone inhibitor CRA-29382

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptase beta-2
A, B, C, D
245Homo sapiensMutation(s): 0 
Gene Names: TPSB2, TPS2
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20231
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C3A
Query on C3A
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
C3A PDBBind:  2FXR Ki: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • 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
HKL-2000data reduction
EPMRphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2006-02-09 
    • Deposition Author(s): Katz, B.A.

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-09
    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