1U6Q

Substituted 2-Naphthamadine inhibitors of Urokinase

• PDB DOI: https://doi.org/10.2210/pdb1U6Q/pdb

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


• Deposited: 2004-07-30 Released: 2004-10-19 
• Deposition Author(s): Bruncko, M., McClellan, W., Wendt, M.D., Sauer, D.R., Geyer, A., Dalton, C.R., Kaminski, M.K., Nienaber, V.L., Rockway, T.R., Giranda, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.290 
• R-Value Work: 0.270 
• R-Value Observed: 0.270 

Literature

Naphthamidine urokinase plasminogen activator inhibitors with improved pharmacokinetic properties.

Bruncko, M., McClellan, W.J., Wendt, M.D., Sauer, D.R., Geyer, A., Dalton, C.R., Kaminski, M.A., Weitzberg, M., Gong, J., Dellaria, J.F., Mantei, R., Zhao, X., Nienaber, V.L., Stewart, K., Klinghofer, V., Bouska, J., Rockway, T.W., Giranda, V.L.

(2005) Bioorg Med Chem Lett 15: 93-98

• PubMed: 15582418 
• DOI: https://doi.org/10.1016/j.bmcl.2004.10.026
• Primary Citation of Related Structures:  
  1U6Q


• PubMed Abstract: 
  

  A series of non-amide-linked 6-substituted-2-naphthamidine urokinase plasminogen activator (uPA) inhibitors are described. These compounds possess excellent binding activities and selectivities with significantly improved pharmacokinetic profiles versus previously described amide-linked inhibitors.

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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: 27.91 kDa 
• Atom Count: 1,955 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
745	B [auth A]	TRANS-6-(2-PHENYLCYCLOPROPYL)-NAPHTHALENE-2-CARBOXAMIDINE C20 H18 N2 NQRIWXVAIWPBEM-OALUTQOASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
745	PDBBind:  1U6Q	Ki: 1310 (nM) from 1 assay(s)
	BindingDB:  1U6Q	Ki: min: 1259, max: 1310 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.290 
• R-Value Work: 0.270 
• R-Value Observed: 0.270 
• 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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-19 
Deposition Author(s): Bruncko, M., McClellan, W., Wendt, M.D., Sauer, D.R., Geyer, A., Dalton, C.R., Kaminski, M.K., Nienaber, V.L., Rockway, T.R., Giranda, V.L.

Revision History  

• Version 1.0: 2004-10-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary