2R2W

Urokinase plasminogen activator B-chain-GPPE complex

• PDB DOI: https://doi.org/10.2210/pdb2R2W/pdb

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


• Deposited: 2007-08-28 Released: 2007-10-23 
• Deposition Author(s): Zeslawska, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.233 
• R-Value Work: 0.199 

Literature

Geometry of GPPE binding to picrate and to the urokinase type plasminogen activator.

Zeslawska, E., Sturzebecher, J., Oleksyn, B.J.

(2007) Bioorg Med Chem Lett 17: 6212-6215

• PubMed: 17905583 
• DOI: https://doi.org/10.1016/j.bmcl.2007.09.020
• Primary Citation of Related Structures:  
  2R2W


• PubMed Abstract: 
  

  Crystal structure of 2-(4-guanidynephenyl)-1-phenyl-ethanone (GPPE) in two different environments was determined in order to compare the binding geometry of these compound to a simple picrate anion and to protein, urokinase-type plasminogen activator (uPA), which may be treated as a target for anti-cancer drugs. It was shown that the conformation and the hydrogen-bonding formation by GPPE molecule are similar in both environments, but several important differences were discovered and described.

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Organizational Affiliation: 

Department of Chemistry, Pedagogical University, ul. Podchorazych 2, 30-084 Kraków, Poland.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 28.79 kDa 
• Atom Count: 2,069 
• Modelled Residue Count: 247 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasminogen activator, urokinase	A [auth U]	253	Homo sapiens	Mutation(s): 1  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
4PG	C [auth U]	1-[4-(2-oxo-2-phenylethyl)phenyl]guanidine C15 H15 N3 O MERNPSIIBFTCAI-UHFFFAOYSA-N
SO4	B [auth U]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
4PG	PDBBind:  2R2W	Ki: 3.40e+4 (nM) from 1 assay(s)
	Binding MOAD:  2R2W	Ki: 3.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.233 
• R-Value Work: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.31	α = 90
b = 54.76	β = 90
c = 82.76	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Zeslawska, E.

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations