3FXZ

Crystal structure of PAK1 kinase domain with ruthenium complex lambda-FL172

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Targeting Large Kinase Active Site with Rigid, Bulky Octahedral Ruthenium Complexes

Maksimoska, J., Feng, L., Harms, K., Yi, C., Kissil, J., Marmorstein, R., Meggers, E.

(2008) J Am Chem Soc 130: 15764-15765

  • DOI: 10.1021/ja805555a
  • Primary Citation of Related Structures:  
    3FXZ, 3FY0

  • PubMed Abstract: 

    • A strategy for targeting protein kinases with large ATP-binding sites by using bulky and rigid octahedral ruthenium complexes as structural scaffolds is presented. A highly potent and selective GSK3 and Pim1 half-sandwich complex NP309 was successfully converted into a PAK1 inhibitor by making use of the large octahedral compounds Lambda-FL172 and Lambda-FL411 in which the cyclopentadienyl moiety of NP309 is replaced by a chloride and sterically demanding diimine ligands ...

    A strategy for targeting protein kinases with large ATP-binding sites by using bulky and rigid octahedral ruthenium complexes as structural scaffolds is presented. A highly potent and selective GSK3 and Pim1 half-sandwich complex NP309 was successfully converted into a PAK1 inhibitor by making use of the large octahedral compounds Lambda-FL172 and Lambda-FL411 in which the cyclopentadienyl moiety of NP309 is replaced by a chloride and sterically demanding diimine ligands. A 1.65 A cocrystal structure of PAK1 with Lambda-FL172 reveals how the large coordination sphere of the ruthenium complex matches the size of the active site and serves as a yardstick to discriminate between otherwise closely related binding sites.

    Organizational Affiliation: 

    The Wistar Institute and University of Pennsylvania, Department of Chemistry, Philadelphia, Pennsylvania 19104, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 1 A297Homo sapiensMutation(s): 1 
Gene Names: PAK1
EC: 2.7.11.1
Find proteins for Q13153 (Homo sapiens)
Explore Q13153 
Go to UniProtKB:  Q13153
NIH Common Fund Data Resources
PHAROS:  Q13153
GTEx:  ENSG00000149269
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLL
Query on FLL
Download Ideal Coordinates CCD File 
A
OCTAHEDRAL RU-PYRIDOCARBAZOLE
C30 H18 Cl F N5 O4 Ru
VQBDWXBWVYJTJT-QQBLGMPTCT		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FLLIC50:  130   nM  Binding MOAD
FLLIC50 :  130   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.183α = 90
b = 103.475β = 90
c = 122.653γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance