Substituted 2-Naphthamidine Inhibitors of Urokinase

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Interaction with the S1beta-pocket of urokinase: 8-heterocycle substituted and 6,8-disubstituted 2-naphthamidine urokinase inhibitors.

Wendt, M.D.Geyer, A.McClellan, W.J.Rockway, T.W.Weitzberg, M.Zhao, X.Mantei, R.Stewart, K.Nienaber, V.Klinghofer, V.Giranda, V.L.

(2004) Bioorg Med Chem Lett 14: 3063-3068

  • DOI: https://doi.org/10.1016/j.bmcl.2004.04.030
  • Primary Citation of Related Structures:  
    1SQA, 1SQO, 1SQT

  • PubMed Abstract: 

    Several 8-substituted 2-naphthamidine-based inhibitors of the serine protease urokinase plasminogen activator (uPA) are described. Direct attachment of five-membered saturated or unsaturated rings improved inhibitor performance; substitution with sulfones further improved binding profiles. Combination of these substituents or of previously described NH-linked heteroaromatic rings with 6-phenyl amide substituents provided further enhancements to potency and selectivity.

  • Organizational Affiliation

    Cancer Research, Global Pharmaceutical R & D, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6101, USA. mike.d.wendt@abbott.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urokinase-type plasminogen activator245Homo sapiensMutation(s): 0 
Gene Names: PLAU
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens)
Explore P00749 
Go to UniProtKB:  P00749
GTEx:  ENSG00000122861 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00749
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
UI2 PDBBind:  1SQO Ki: 35 (nM) from 1 assay(s)
BindingDB:  1SQO Ki: min: 30, max: 35 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.84 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.16α = 90
b = 53β = 90
c = 82.3γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance