1BTW

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: 1.70 Å
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

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

  • DOI: 10.1021/bi00026a008
  • Primary Citation of Related Structures:  
    1BTZ, 1BTY, 1BTX, 1BTW

  • 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 transition-state analogs and incorporate additional groups that can be utilized for selectivity between proteases ...

    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
    • 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
    • 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 B 33: 1824
    • 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 Harb Symp Quant Biol 36: 125

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-TRYPSINA229Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0ZW
Query on 0ZW

Download CCD File 
A
N-(tert-butoxycarbonyl)-L-alanyl-N-{(1S)-5-ammonio-1-[hydroxy(3-hydroxypropoxy)boranyl]pentyl}-L-valinamide
C21 H44 B N4 O7
JPOFXBAJTXFLAJ-ULQDDVLXSA-O
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000388 (0ZW)
Query on PRD_000388
AT-BUTOXY-ALA-VAL-BORO-LYS 1,3-PROPANEDIOL MONOESTERPeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.74α = 90
b = 63.54β = 90
c = 68.93γ = 90
Software Package:
Software NamePurpose
RAXISdata collection
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other