Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

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This is version 1.2 of the entry. See complete history


Design of potent selective zinc-mediated serine protease inhibitors.

Katz, B.A.Clark, J.M.Finer-Moore, J.S.Jenkins, T.E.Johnson, C.R.Ross, M.J.Luong, C.Moore, W.R.Stroud, R.M.

(1998) Nature 391: 608-612

  • DOI: https://doi.org/10.1038/35422
  • Primary Citation of Related Structures:  
    1C1N, 1C1O, 1C1P, 1C1Q, 1C1R, 1C1T, 1C1U, 1C1V, 1C1W, 1C2D, 1C2E, 1C2F, 1C2G, 1C2H, 1C2I, 1C2J, 1C2K, 1C2L, 1C2M, 1XUF, 1XUG, 1XUH, 1XUI, 1XUJ, 1XUK

  • PubMed Abstract: 

    Many serine proteases are targets for therapeutic intervention because they often play key roles in disease. Small molecule inhibitors of serine proteases with high affinity are especially interesting as they could be used as scaffolds from which to develop drugs selective for protease targets. One such inhibitor is bis(5-amidino-2-benzimidazolyl)methane (BABIM), standing out as the best inhibitor of trypsin (by a factor of over 100) in a series of over 60 relatively closely related analogues. By probing the structural basis of inhibition, we discovered, using crystallographic methods, a new mode of high-affinity binding in which a Zn2+ ion is tetrahedrally coordinated between two chelating nitrogens of BABIM and two active site residues, His57 and Ser 195. Zn2+, at subphysiological levels, enhances inhibition by over 10(3)-fold. The distinct Zn2+ coordination geometry implies a strong dependence of affinity on substituents. This unique structural paradigm has enabled development of potent, highly selective, Zn2+-dependent inhibitors of several therapeutically important serine proteases, using a physiologically ubiquitous metal ion.

  • Organizational Affiliation

    Arris Pharmaceutical Corporation, South San Francisco, California 94080, USA. bak@arris.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRYPSIN223Bos taurusMutation(s): 0 
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.96α = 90
b = 54.96β = 90
c = 109.12γ = 120
Software Package:
Software NamePurpose
BIOTEXdata collection
X-PLORmodel building
BIOTEXdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance