1C2I

RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1038/35422
  • Primary Citation of Related Structures:  1C1N, 1C1O, 1C1P, 1C1Q, 1C1R, 1C1T, 1C1U, 1C1V, 1C1W, 1C2D, 1C2E, 1C2F, 1C2G, 1C2H, 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
A
223Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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

Download SDF File 
Download CCD File 
A
BIS(5-AMIDINO-2-BENZIMIDAZOLYL)METHANE KETONE
C17 H16 N8 O
VVVXDHROXQUONB-UHFFFAOYSA-P
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.000α = 90.00
b = 55.000β = 90.00
c = 109.760γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
bioteXdata collection
X-PLORrefinement
bioteXdata reduction
Insight IImodel building
Quantamodel building
bioteXdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-07-21 
  • Released Date: 2000-07-26 
  • Deposition Author(s): Katz, B.A., Luong, C.

Revision History 

  • Version 1.0: 2000-07-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description