2R2W

Urokinase plasminogen activator B-chain-GPPE complex


Experimental Data Snapshot

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

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plasminogen activator, urokinaseA [auth U]253Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4PG (Subject of Investigation/LOI)
Query on 4PG

Download Ideal Coordinates CCD File 
C [auth U]1-[4-(2-oxo-2-phenylethyl)phenyl]guanidine
C15 H15 N3 O
MERNPSIIBFTCAI-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth U]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 53.31α = 90
b = 54.76β = 90
c = 82.76γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance