4G8O

Crystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic characterization and crystal structure of a small molecule inactivator bound to plasminogen activator inhibitor-1.

Li, S.H.Reinke, A.A.Sanders, K.L.Emal, C.D.Whisstock, J.C.Stuckey, J.A.Lawrence, D.A.

(2013) Proc.Natl.Acad.Sci.USA 110: E4941-E4949

  • DOI: 10.1073/pnas.1216499110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plasminogen activator inhibitor type-1 (PAI-1) is a member of the serine protease inhibitor (serpin) family. Excessive PAI-1 activity is associated with human disease, making it an attractive pharmaceutical target. However, like other serpins, PAI-1 ...

    Plasminogen activator inhibitor type-1 (PAI-1) is a member of the serine protease inhibitor (serpin) family. Excessive PAI-1 activity is associated with human disease, making it an attractive pharmaceutical target. However, like other serpins, PAI-1 has a labile structure, making it a difficult target for the development of small molecule inhibitors, and to date, there are no US Food and Drug Administration-approved small molecule inactivators of any serpins. Here we describe the mechanistic and structural characterization of a high affinity inactivator of PAI-1. This molecule binds to PAI-1 reversibly and acts through an allosteric mechanism that inhibits PAI-1 binding to proteases and to its cofactor vitronectin. The binding site is identified by X-ray crystallography and mutagenesis as a pocket at the interface of β-sheets B and C and α-helix H. A similar pocket is present on other serpins, suggesting that this site could be a common target in this structurally conserved protein family.


    Organizational Affiliation

    Departments of Pathology and Internal Medicine, Division of Cardiovascular Medicine, University of Michigan Medical School, Ann Arbor, MI 48109.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasminogen activator inhibitor 1
A, B, C, D
376Homo sapiensMutation(s): 4 
Gene Names: SERPINE1 (PAI1, PLANH1)
Find proteins for P05121 (Homo sapiens)
Go to Gene View: SERPINE1
Go to UniProtKB:  P05121
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
96P
Query on 96P

Download SDF File 
Download CCD File 
D
(2S)-3-({[3-(trifluoromethyl)phenoxy]carbonyl}amino)propane-1,2-diyl bis(3,4,5-trihydroxybenzoate)
C25 H20 F3 N O12
OXWKLJPAKUDPJY-HNNXBMFYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
96PKd: 22 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.239 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 65.335α = 91.32
b = 75.317β = 93.49
c = 105.002γ = 115.65
Software Package:
Software NamePurpose
HKL-2000data scaling
MD2data collection
DENZOdata reduction
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-01
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Refinement description