6D3Y

Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma.

Swedberg, J.E.Wu, G.Mahatmanto, T.Durek, T.Caradoc-Davies, T.T.Whisstock, J.C.Law, R.H.P.Craik, D.J.

(2019) J. Med. Chem. 62: 552-560

  • DOI: 10.1021/acs.jmedchem.8b01139
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antifibrinolytic drugs provide important pharmacological interventions to reduce morbidity and mortality from excessive bleeding during surgery and after trauma. Current drugs used for inhibiting the dissolution of fibrin, the main structural compone ...

    Antifibrinolytic drugs provide important pharmacological interventions to reduce morbidity and mortality from excessive bleeding during surgery and after trauma. Current drugs used for inhibiting the dissolution of fibrin, the main structural component of blood clots, are associated with adverse events due to lack of potency, high doses and non-selective inhibition mechanisms. These deficiencies warrant the development of a new generation highly potent and selective fibrinolysis inhibitors. Here we use the 14-amino acid backbone-cyclic sunflower trypsin inhibitor-1 scaffold to design a highly potent (Ki = 0.05 nM) inhibitor of the primary serine protease in fibrinolysis, plasmin. This compound displays a million-fold selectivity over other serine proteases in blood, inhibits fibrinolysis in plasma more effectively than the gold-standard therapeutic inhibitor aprotinin and is a promising candidate for development of highly specific fibrinolysis inhibitors with reduced side effects.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasminogen
A
247Homo sapiensMutation(s): 0 
Gene Names: PLG
EC: 3.4.21.7
Find proteins for P00747 (Homo sapiens)
Go to Gene View: PLG
Go to UniProtKB:  P00747
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Trypsin inhibitor 1
C
14Helianthus annuusMutation(s): 1 
Gene Names: sfti1
Find proteins for Q4GWU5 (Helianthus annuus)
Go to UniProtKB:  Q4GWU5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.905α = 90.00
b = 41.506β = 109.63
c = 79.527γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-04-17 
  • Released Date: 2019-01-23 
  • Deposition Author(s): Law, R.H.P., Wu, G.

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-05-01
    Type: Data collection, Database references