1SZM

DUAL BINDING MODE OF BISINDOLYLMALEIMIDE 2 TO PROTEIN KINASE A (PKA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The protein kinase C inhibitor bisindolyl maleimide 2 binds with reversed orientations to different conformations of protein kinase a.

Gassel, M.Breitenlechner, C.B.Koenig, N.Huber, R.Engh, R.A.Bossemeyer, D.

(2004) J.Biol.Chem. 279: 23679-23690

  • DOI: 10.1074/jbc.M314082200

  • PubMed Abstract: 
  • As the key mediators of eukaryotic signal transduction, the protein kinases often cause disease, and in particular cancer, when disregulated. Appropriately selective protein kinase inhibitors are sought after as research tools and as therapeutic drug ...

    As the key mediators of eukaryotic signal transduction, the protein kinases often cause disease, and in particular cancer, when disregulated. Appropriately selective protein kinase inhibitors are sought after as research tools and as therapeutic drugs; several have already proven valuable in clinical use. The AGC subfamily protein kinase C (PKC) was identified early as a cause of cancer, leading to the discovery of a variety of PKC inhibitors. Despite its importance and early discovery, no crystal structure for PKC has yet been reported. Therefore, we have co-crystallized PKC inhibitor bisindolyl maleimide 2 (BIM2) with PKA variants to study its binding interactions. BIM2 co-crystallized as an asymmetric pair of kinase-inhibitor complexes. In this asymmetric unit, the two kinase domains have different lobe configurations, and two different inhibitor conformers bind in different orientations. One kinase molecule (A) is partially open with respect to the catalytic conformation, the other (B) represents the most open conformation of PKA reported so far. In monomer A, the BIM2 inhibitor binds tightly via an induced fit in the ATP pocket. The indole moieties are rotated out of the plane with respect to the chemically related but planar inhibitor staurosporine. In molecule B a different conformer of BIM2 binds in a reversed orientation relative to the equivalent maleimide atoms in molecule A. Also, a critical active site salt bridge is disrupted, usually indicating the induction of an inactive conformation. Molecular modeling of the clinical phase III PKC inhibitor LY333531 into the electron density of BIM2 reveals the probable binding mechanism and explains selectivity properties of the inhibitor.


    Related Citations: 
    • Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential.
      Prade, L.,Engh, R.A.,Girod, A.,Kinzel, V.,Huber, R.,Bossemeyer, D.
      (1997) Structure 5: 1627


    Organizational Affiliation

    Department of Pathochemistry, German Cancer Research Center, 69120 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase, alpha-catalytic subunit
A, B
350Bos taurusGene Names: PRKACA
EC: 2.7.11.11
Find proteins for P00517 (Bos taurus)
Go to Gene View: PRKACA
Go to UniProtKB:  P00517
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BI4
Query on BI4

Download SDF File 
Download CCD File 
A, B
3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE
C27 H26 N4 O2
LBFDERUQORUFIN-KRWDZBQOSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BI4IC50: 6350 nM BINDINGMOAD
BI2IC50: 2940 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.065α = 90.00
b = 89.005β = 90.00
c = 116.388γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4phasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance