4AQH

Plasminogen activator inhibitor type-1 in complex with the inhibitor AZ3976


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of a Small Molecule Inhibitor of Plasminogen Activator Inhibitor Type 1 that Accelerates the Transition Into the Latent Conformation

Fjellstrom, O.Deinum, J.Sjogren, T.Johansson, C.Geschwindner, S.Nerme, V.Legnehed, A.Mcpheat, J.Olsson, K.Bodin, C.Panuovic, A.Gustafsson, D.

(2013) J.Biol.Chem. 288: 873

  • DOI: 10.1074/jbc.M112.371732

  • PubMed Abstract: 
  • A novel class of small molecule inhibitors for plasminogen activator inhibitor type 1 (PAI-1), represented by AZ3976, was identified in a high throughput screening campaign. AZ3976 displayed an IC(50) value of 26 μm in an enzymatic chromogenic assay. ...

    A novel class of small molecule inhibitors for plasminogen activator inhibitor type 1 (PAI-1), represented by AZ3976, was identified in a high throughput screening campaign. AZ3976 displayed an IC(50) value of 26 μm in an enzymatic chromogenic assay. In a plasma clot lysis assay, the compound was active with an IC(50) of 16 μm. Surprisingly, AZ3976 did not bind to active PAI-1 but bound to latent PAI-1 with a K(D) of 0.29 μm at 35 °C and a binding stoichiometry of 0.94, as measured by isothermal calorimetry. Reversible binding was confirmed by surface plasmon resonance direct binding experiments. The x-ray structure of AZ3976 in complex with latent PAI-1 was determined at 2.4 Å resolution. The inhibitor was bound in the flexible joint region with the entrance to the cavity located between α-helix D and β-strand 2A. A set of surface plasmon resonance experiments revealed that AZ3976 inhibited PAI-1 by enhancing the latency transition of active PAI-1. Because AZ3976 only had measurable affinity for latent PAI-1, we propose that its mechanism of inhibition is based on binding to a small fraction in equilibrium with active PAI-1, a latent-like prelatent form, from which latent PAI-1 is then generated more rapidly. This mode of action, with induced accelerated latency transition of active PAI-1 may, together with supporting x-ray data, provide improved opportunities for small molecule drug design in the hunt for therapeutically useful PAI-1 inhibitors.


    Organizational Affiliation

    Department of Medicinal Chemistry, AstraZeneca R&D Mölndal, S-431 83 Mölndal, Sweden. ola.fjellstrom@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLASMINOGEN ACTIVATOR INHIBITOR 1
A, B, C
383Homo sapiensMutation(s): 0 
Gene Names: SERPINE1 (PAI1, PLANH1)
Find proteins for P05121 (Homo sapiens)
Go to Gene View: SERPINE1
Go to UniProtKB:  P05121
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TB7
Query on TB7

Download SDF File 
Download CCD File 
A, B, C
TERT-BUTYL 3-[(4-OXO-3H-PYRIDO[2,3-D]PYRIMIDIN-2-YL)AMINO]AZETIDINE-1-CARBOXYLATE
C15 H19 N5 O3
CKUDSTVQYFRZJW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TB7Kd: 290 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.157 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 119.399α = 90.00
b = 119.399β = 90.00
c = 99.691γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-01-16
    Type: Database references
  • Version 1.2: 2013-01-30
    Type: Database references