Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.01 kDa 
• Atom Count: 1962 
• Modelled Residue Count: 245 
• Deposited Residue Count: 245 
• Unique protein chains: 1

1OWJ

Substituted 2-Naphthamidine Inhibitors of Urokinase

• PDB DOI: 10.2210/pdb1OWJ/pdb

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


• Deposited: 2003-03-28 Released: 2003-09-30 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.344 
• R-Value Work: 0.253 
• R-Value Observed: 0.253 

Literature

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

• PubMed: 14711304 
• DOI: 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.

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Organizational Affiliation: 

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

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
155	B [auth A]	6-[(Z)-AMINO(IMINO)METHYL]-N-(1-ISOPROPYL-3,4-DIHYDROISOQUINOLIN-7-YL)-2-NAPHTHAMIDE C24 H24 N4 O XRHANBWAKSYPEN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
155	PDBBind:  1OWJ	Ki: 48 (nM) from 1 assay(s)
	BindingDB:  1OWJ	Ki: min: 48, max: 50 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.344 
• R-Value Work: 0.253 
• R-Value Observed: 0.253 
• 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
MAR345	data collection
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-28 
• Released Date: 2003-09-30 
Deposition Author(s): 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.

Revision History  

• 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