3IG6

Low molecular weigth human Urokinase type Plasminogen activator 2-[6-(3'-Aminomethyl-biphenyl-3-yloxy)-4-(3-dimethylamino-pyrrolidin-1-yl)-3,5-difluoro-pyridin-2-yloxy]-4-dimethylamino-benzoic acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of orally bioavailable, non-amidine inhibitors of Urokinase Plasminogen Activator (uPA)

West, C.W.Adler, M.Arnaiz, D.Chen, D.Chu, K.Gualtieri, G.Ho, E.Huwe, C.Light, D.Phillips, G.Pulk, R.Sukovich, D.Whitlow, M.Yuan, S.Bryant, J.

(2009) Bioorg Med Chem Lett 19: 5712-5715

  • DOI: 10.1016/j.bmcl.2009.08.008
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In this Letter we report the synthesis and evaluation of a series of non-amidine inhibitors of Urokinase Plasminogen Activator (uPA). Starting from compound 1, a significant change provided compounds in which the amidine, binding in the S1 pocket, wa ...

    In this Letter we report the synthesis and evaluation of a series of non-amidine inhibitors of Urokinase Plasminogen Activator (uPA). Starting from compound 1, a significant change provided compounds in which the amidine, binding in the S1 pocket, was replaced with a primary amine. Further modifications led to the identification of potent, selective, and orally bioavailable uPA inhibitors.


    Organizational Affiliation

    Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States. cwest@icagen.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urokinase-type plasminogen activatorA, C23Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
Explore P00749 
Go to UniProtKB:  P00749
NIH Common Fund Data Resources
PHAROS  P00749
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Urokinase-type plasminogen activatorB, D253Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
Explore P00749 
Go to UniProtKB:  P00749
NIH Common Fund Data Resources
PHAROS  P00749
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
438
Query on 438

Download CCD File 
B, D
2-[(6-{[3'-(aminomethyl)biphenyl-3-yl]oxy}-4-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]-3,5-difluoropyridin-2-yl)oxy]-4-(dimethylamino)benzoic acid
C33 H35 F2 N5 O4
WIFBOPRNBMRLLS-XMMPIXPASA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
438IC50:  25   nM  BindingDB
438IC50:  25   nM  Binding MOAD
438IC50 :  25   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.855α = 90
b = 52.294β = 90.23
c = 72.58γ = 90
Software Package:
Software NamePurpose
BOSdata collection
CNXrefinement
XTALVIEWrefinement
X-GENdata reduction
X-GENdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-07-27 
  • Released Date: 2009-10-13 
  • Deposition Author(s): Adler, M., Whitlow, M.

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Atomic model