2VIV

Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator

• PDB DOI: https://doi.org/10.2210/pdb2VIV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-12-05 Released: 2008-01-22 
• Deposition Author(s): Frederickson, M., Callaghan, O., Chessari, G., Congreve, M., Cowan, S.R., Matthews, J.E., McMenamin, R., Smith, D., Vinkovic, M., Wallis, N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.238 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Literature

Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator.

Frederickson, M., Callaghan, O., Chessari, G., Congreve, M., Cowan, S.R., Matthews, J.E., Mcmenamin, R., Smith, D., Vinkovic, M., Wallis, N.G.

(2008) J Med Chem 51: 183

• PubMed: 18163548 
• DOI: https://doi.org/10.1021/jm701359z
• Primary Citation of Related Structures:  
  2VIN, 2VIO, 2VIP, 2VIQ, 2VIV, 2VIW


• PubMed Abstract: 
  

  Fragment-based lead discovery has been applied to urokinase-type plasminogen activator (uPA). The (R)-enantiomer of the orally active drug mexiletine 5 (a fragment hit from X-ray crystallographic screening) was the chemical starting point. Structure-aided design led to elaborated inhibitors that retained the key interactions of (R)-5 while gaining extra potency by simultaneously occupying neighboring regions of the active site. Subsequent optimization led to 15, a potent, selective, and orally bioavailable inhibitor of uPA.

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Organizational Affiliation: 

Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 28.91 kDa 
• Atom Count: 2,218 
• Modelled Residue Count: 248 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B	A	253	Homo sapiens	Mutation(s): 2  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
VG2	C [auth A]	4-(2-aminoethoxy)-N-(3-chloro-5-piperidin-1-ylphenyl)-3,5-dimethylbenzamide C22 H28 Cl N3 O2 JDYIYIRPQKMWMM-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
VG2	PDBBind:  2VIV	IC50: 520 (nM) from 1 assay(s)
	BindingDB:  2VIV	IC50: 520 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.238 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.338	α = 90
b = 54.001	β = 90
c = 81.938	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-22 
Deposition Author(s): Frederickson, M., Callaghan, O., Chessari, G., Congreve, M., Cowan, S.R., Matthews, J.E., McMenamin, R., Smith, D., Vinkovic, M., Wallis, N.G.

Revision History  

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Other, Structure summary