1SQA | pdb_00001sqa

Substituted 2-Naphthamidine Inhibitors of Urokinase

• PDB DOI: https://doi.org/10.2210/pdb1SQA/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2004-03-18 Released: 2004-04-27 
• Deposition Author(s): Wendt, M.D., Geyer, A., McClellan, W.J., Rockway, T.W., Weitzberg, M., Zhao, X., Stewart, K., Nienaber, V., Klinghofer, V., Giranda, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.266 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

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

• PubMed: 15149645 
• 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.

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Organizational Affiliation: 

Cancer Research, Global Pharmaceutical R & D, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6101, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.34 kDa 
• Atom Count: 2,041 
• Modelled Residue Count: 245 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A	245	Homo sapiens	Mutation(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 GTEx:  ENSG00000122861

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UI1	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
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
UI1	BindingDB:  1SQA	Ki: min: 0.62, max: 0.63 (nM) from 2 assay(s)
		IC50: 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 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.16	α = 90
b = 53	β = 90
c = 82.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-27 
Deposition Author(s): Wendt, M.D., Geyer, A., McClellan, W.J., Rockway, T.W., Weitzberg, M., Zhao, X., Stewart, K., Nienaber, V., Klinghofer, V., Giranda, V.L.

Revision History  

• 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
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary