Substituted 2-Naphthamidine Inhibitors of Urokinase

Experimental Data Snapshot

  • Resolution: 2.93 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.286 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Identification of Novel Binding Interactions in the Development of Potent, Selective 2-Naphthamidine Inhibitors of Urokinase. Synthesis, Structural Analysis, and SAR of N-Phenyl Amide 6-Substitution.

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

(2004) J Med Chem 47: 303-324

  • DOI: https://doi.org/10.1021/jm0300072
  • Primary Citation of Related Structures:  
    1OWD, 1OWE, 1OWH, 1OWI, 1OWJ, 1OWK

  • PubMed Abstract: 

    The preparation and assessment of biological activity of 6-substituted 2-naphthamidine inhibitors of the serine protease urokinase plasminogen activator (uPA, or urokinase) is described. 2-Naphthamidine was chosen as a starting point based on synthetic considerations and on modeling of substituent vectors. Phenyl amides at the 6-position were found to improve binding; replacement of the amide with other two-atom linkers proved ineffective. The phenyl group itself is situated near the S1' subsite; substitutions off of the phenyl group accessed S1' and other distant binding regions. Three new points of interaction were defined and explored through ring substitution. A solvent-exposed salt bridge with the Asp60A carboxylate was formed using a 4-alkylamino group, improving affinity to K(i) = 40 nM. Inhibitors also accessed two hydrophobic regions. One interaction is characterized by a tight hydrophobic fit made with a small dimple largely defined by His57 and His99; a weaker, less specific interaction involves alkyl groups reaching into the broad prime-side protein binding region near Val41 and the Cys42-Cys58 disulfide, displacing water molecules and leading to small gains in activity. Many inhibitors accessed two of these three regions. Affinities range as low as K(i) = 6 nM, and many compounds had K(i) < 100 nM, while moderate to excellent selectivity was gained versus four of five members of a panel of relevant serine proteases. Also, some selectivity against trypsin was generated via the interaction with Asp60A. X-ray structures of many of these compounds were used to inform our inhibitor design and to increase our understanding of key interactions. In combination with our exploration of 8-substitution patterns, we have identified a number of novel binding interactions for uPA inhibitors.

  • Organizational Affiliation

    Cancer Research and Structural Biology, Global Pharmaceutical R & D, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 426

Download Ideal Coordinates CCD File 
C23 H23 N3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
426 BindingDB:  1OWI Ki: min: 25, max: 28 (nM) from 2 assay(s)
PDBBind:  1OWI Ki: 28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.93 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.286 
  • 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
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description