3QN7

Potent and selective bicyclic peptide inhibitor (UK18) of human urokinase-type plasminogen activator(uPA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bicyclic peptide inhibitor reveals large contact interface with a protease target

Angelini, A.Cendron, L.Chen, S.Touati, J.Winter, G.Zanotti, G.Heinis, C.

(2012) Acs Chem.Biol. 7: 817-821

  • DOI: 10.1021/cb200478t

  • PubMed Abstract: 
  • From a large combinatorial library of chemically constrained bicyclic peptides we isolated a selective and potent (K(i) = 53 nM) inhibitor of human urokinase-type plasminogen activator (uPA) and crystallized the complex. This revealed an extended str ...

    From a large combinatorial library of chemically constrained bicyclic peptides we isolated a selective and potent (K(i) = 53 nM) inhibitor of human urokinase-type plasminogen activator (uPA) and crystallized the complex. This revealed an extended structure of the peptide with both peptide loops engaging the target to form a large interaction surface of 701 Å(2) with multiple hydrogen bonds and complementary charge interactions, explaining the high affinity and specificity of the inhibitor. The interface resembles that between two proteins and suggests that these constrained peptides have the potential to act as small protein mimics.


    Related Citations: 
    • Structural basis of specificity of a peptidyl urokinase inhibitor, upain-1
      Zhao, G.,Yuan, C.,Wind, T.,Huang, Z.,Andreasen, P.A.,Huang, M.
      (2007) J.Struct.Biol. 160: 1
    • The crystal structure of the catalytic domain of human urokinase-type plasminogen activator
      Spraggon, G.,Phillips, C.,Nowak, U.K.,Ponting, C.P.,Saunders, D.,Dobson, C.M.,Stuart, D.I.,Jones, E.Y.
      (1995) Structure 3: 681


    Organizational Affiliation

    Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urokinase-type plasminogen activator
A
253Homo sapiensMutation(s): 2 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
Go to Gene View: PLAU
Go to UniProtKB:  P00749
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bicyclic peptide inhibitor
B
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZBR
Query on ZBR

Download SDF File 
Download CCD File 
B
1,3,5-tris(bromomethyl)benzene
C9 H9 Br3
GHITVUOBZBZMND-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 121.250α = 90.00
b = 121.250β = 90.00
c = 42.720γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
SCALAdata scaling
PHASESphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2013-04-10
    Type: Database references