1XH4

Crystal Structures of Protein Kinase B Selective Inhibitors in Complex with Protein Kinase A and Mutants


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design and crystal structures of protein kinase B-selective inhibitors in complex with protein kinase A and mutants

Breitenlechner, C.B.Friebe, W.-G.Brunet, E.Werner, G.Graul, K.Thomas, U.Kuenkele, K.-P.Schaefer, W.Gassel, M.Bossemeyer, D.Huber, R.Engh, R.A.Masjost, B.

(2005) J Med Chem 48: 163-170

  • DOI: 10.1021/jm049701n
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein kinase B (PKB)-selective inhibitors were designed, synthesized, and cocrystallized using the AGC kinase family protein kinase A (PKA, often called cAMP-dependent protein kinase); PKA has been used as a surrogate for other members of this family and indeed for protein kinases in general ...

    Protein kinase B (PKB)-selective inhibitors were designed, synthesized, and cocrystallized using the AGC kinase family protein kinase A (PKA, often called cAMP-dependent protein kinase); PKA has been used as a surrogate for other members of this family and indeed for protein kinases in general. The high homology between PKA and PKB includes very similar ATP binding sites and hence similar binding pockets for inhibitors, with only few amino acids that differ between the two kinases. A series of these sites were mutated in PKA in order to improve the surrogate model for a design of PKB-selective inhibitors. Namely, the PKA to PKB exchanges F187L and Q84E enable the design of the selective inhibitors described herein which mimic ATP but extend further into a site not occupied by ATP. In this pocket, selectivity over PKA can be achieved by the introduction of bulkier substituents. Analysis of the cocrystal structures and binding studies were performed to rationalize the selectivity and improve the design.


    Related Citations: 
    • Structure-based optimization of novel azepane derivatives as PKB inhibitors
      Breitenlechner, C.B., Wegge, T., Berillon, L., Graul, K., Marzenell, K., Friebe, W.-G., Thomas, U., Schumacher, R., Huber, R., Engh, R.A., Masjost, B.
      (2004) J Med Chem 47: 1375

    Organizational Affiliation

    Abteilung Strukturforschung, Max-Planck-Institut fuer Biochemie, 82152 Martinsried, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase, alpha-catalytic subunitA350Bos taurusMutation(s): 3 
Gene Names: PRKACA
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
Find proteins for P00517 (Bos taurus)
Explore P00517 
Go to UniProtKB:  P00517
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase inhibitor, alpha formB20N/AMutation(s): 0 
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
NIH Common Fund Data Resources
PHAROS  P61925
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R69
Query on R69

Download CCD File 
A
N-[4-({4-[5-(DIMETHYLAMINO)-2-HYDROXYBENZOYL]BENZOYL}AMINO)AZEPAN-3-YL]ISONICOTINAMIDE
C28 H31 N5 O4
NYQLXXDGJNYPPH-DNQXCXABSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R69Kd:  34   nM  Binding MOAD
R69IC50:  30   nM  BindingDB
R69Kd :  34   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.013α = 90
b = 79.144β = 90
c = 79.643γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance