1SQA

Substituted 2-Naphthamidine Inhibitors of Urokinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

  • 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase-type plasminogen activatorA245Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens)
Explore P00749 
Go to UniProtKB:  P00749
PHAROS:  P00749
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UI1 (Subject of Investigation/LOI)
Query on UI1

Download Ideal Coordinates CCD File 
E [auth A]6-[(Z)-AMINO(IMINO)METHYL]-N-[4-(AMINOMETHYL)PHENYL]-4-(PYRIMIDIN-2-YLAMINO)-2-NAPHTHAMIDE
C23 H21 N7 O
CSWQJKHBMACTGB-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
UI1 BindingDB:  1SQA Ki: min: 0.62, max: 0.63 (nM) from 2 assay(s)
IC50: 620 (nM) from 1 assay(s)
Binding MOAD:  1SQA Ki: 0.62 (nM) from 1 assay(s)
PDBBind:  1SQA Ki: 0.62 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • 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
X-PLORrefinement

Structure Validation

View Full Validation Report



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