3IG6 | pdb_00003ig6

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

• PDB DOI: https://doi.org/10.2210/pdb3IG6/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.228 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

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

• PubMed: 19703768 
• DOI: https://doi.org/10.1016/j.bmcl.2009.08.008
• Primary Citation Related Structures: 
  3IG6


• 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, was replaced with a primary amine. Further modifications led to the identification of potent, selective, and orally bioavailable uPA inhibitors.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, United States. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B1C1D1E1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.64 kDa 
• Atom Count: 4,259 
• Modeled Residue Count: 500 
• Deposited Residue Count: 552 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A, C	23	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	B, D	253	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
438	E [auth B], F [auth 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
PO4	G [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.228 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.855	α = 90
b = 52.294	β = 90.23
c = 72.58	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
CNX	refinement
XTALVIEW	refinement
X-GEN	data reduction
X-GEN	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary