4CIK

plasminogen kringle 1 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of the Fibrinolysis Inhibitor Azd6564, Acting Via Interference of a Protein-Protein Interaction.

Cheng, L.Pettersen, D.Ohlsson, B.Schell, P.Karle, M.Evertsson, E.Pahlen, S.Jonforsen, M.Plowright, A.T.Bostrom, J.Fex, T.Thelin, A.Hilgendorf, C.Xue, Y.Wahlund, G.Lindberg, W.Larsson, L.Gustafsson, D.

(2014) ACS Med Chem Lett 5: 538

  • DOI: https://doi.org/10.1021/ml400526d
  • Primary Citation of Related Structures:  
    4CIK

  • PubMed Abstract: 

    A class of novel oral fibrinolysis inhibitors has been discovered, which are lysine mimetics containing an isoxazolone as a carboxylic acid isostere. As evidenced by X-ray crystallography the inhibitors bind to the lysine binding site in plasmin thus preventing plasmin from binding to fibrin, hence blocking the protein-protein interaction. Optimization of the series, focusing on potency in human buffer and plasma clotlysis assays, permeability, and GABAa selectivity, led to the discovery of AZD6564 (19) displaying an in vitro human plasma clot lysis IC50 of 0.44 μM, no detectable activity against GABAa, and with DMPK properties leading to a predicted dose of 340 mg twice a day oral dosing in humans.


  • Organizational Affiliation

    Medicinal Chemistry, CVMD iMED, Bioscience, CVMD iMED, DMPK, CVMD iMED, and Discovery Sciences, AstraZeneca Mölndal , SE-43183 Mölndal, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLASMINOGEN83Homo sapiensMutation(s): 0 
EC: 3.4.21.7
UniProt & NIH Common Fund Data Resources
Find proteins for P00747 (Homo sapiens)
Explore P00747 
Go to UniProtKB:  P00747
PHAROS:  P00747
GTEx:  ENSG00000122194 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00747
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XO3
Query on XO3

Download Ideal Coordinates CCD File 
B [auth A]5-[(2R,4S)-2-(phenylmethyl)piperidin-4-yl]-1,2-oxazol-3-one
C15 H18 N2 O2
LNFPEBXLWIXQLF-STQMWFEESA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
XO3 BindingDB:  4CIK IC50: min: 280, max: 950 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.777α = 90
b = 57.594β = 90
c = 81.414γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description