1BTX

Episelection: Novel Ki ~Nanomolar Inhibitors of Serine Proteases Selected by Binding or Chemistry on an Enzyme Surface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface.

Katz, B.A.Finer-Moore, J.Mortezaei, R.Rich, D.H.Stroud, R.M.

(1995) Biochemistry 34: 8264-8280

  • Primary Citation of Related Structures:  1BTW, 1BTY, 1BTZ

  • PubMed Abstract: 
  • A novel class of mechanism-based inhibitors of the serine proteases is developed using epitaxial selection. Tripeptide boronates esterified by an alcohol or alcohols at the boron retain the tight binding to trypsin-like enzymes associated with transi ...

    A novel class of mechanism-based inhibitors of the serine proteases is developed using epitaxial selection. Tripeptide boronates esterified by an alcohol or alcohols at the boron retain the tight binding to trypsin-like enzymes associated with transition-state analogs and incorporate additional groups that can be utilized for selectivity between proteases. Formed by reaction of a series of alcohols with the inhibitor boronate oxygen(s), the most structurally compatible alcohol-derivatized inhibitors are either selected by binding to the enzyme (epitaxial selection) or assembled by epitaxial reaction on the enzyme surface. Mass spectrometry of the derivatized boronates and X-ray crystallography of the complexes identify the chemical structures and the three-dimensional interactions of inhibitors generated. This scheme also engineers novel, potent (Ki approximately 7 nM), and more specific inhibitors of individual serine proteases, by derivitizations of compounds obtained by epitaxial selection.


    Related Citations: 
    • Solvent Structure in Crystals of Trypsin Determined by X-Ray and Neutron Diffraction
      Finer-Moore, J.S.,Kossiakoff, A.,Hurley, J.H.,Earnest, T.,Stroud, R.M.
      (1992) Proteins 12: 203
    • Structure and Specific Binding of Trypsin, Comparison of Inhibited Derivatives and a Model for Substrate Binding
      Krieger, M.,Kay, L.M.,Stroud, R.M.
      (1974) J.Mol.Biol. 83: 209
    • The Crystal and Molecular Structure of Dip-Inhibited Bovine Trypsin at 2.7 Angstroms Resolution
      Stroud, R.M.,Kay, L.M.,Dickerson, R.E.
      (1972) Cold Spring Harbor Symp.Quant.Biol. 36: 125
    • Difference Fourier Refinement of the Structure of Dip-Trypsin at 1.5 Angstroms Using a Minicomputer Technique
      Chambers, J.L.,Stroud, R.M.
      (1977) Acta Crystallogr.,Sect.B 33: 1824
    • 1.59 Angstrom Structure of Trypsin at 120K: Comparison of Low Temperature and Room Temperature Structures
      Earnest, T.,Fauman, E.,Craik, C.S.,Stroud, R.M.
      (1991) Proteins 10: 171


    Organizational Affiliation

    Arris Pharmaceutical Corporation, South San Francisco, California 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-TRYPSIN
A
229Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
0ZX
Query on 0ZX

Download SDF File 
Download CCD File 
A
N-(tert-butoxycarbonyl)-L-alanyl-N-[(1S)-5-amino-1-(diethoxyboranyl)pentyl]-L-valinamide
C22 H45 B N4 O6
GIVAJOGGLRHKIW-BZSNNMDCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000389 (0ZX)
Query on PRD_000389
AT-BUTOXY-ALA-VAL-BORO-LYS ETHYL ESTERPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.840α = 90.00
b = 58.610β = 90.00
c = 67.470γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other