1XH5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1021/jm049701n
  • Primary Citation of Related Structures:  
    1XH4, 1XH5, 1XH6, 1XH7, 1XH8, 1XH9, 1XHA

  • 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. 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase, alpha-catalytic subunit350Bos taurusMutation(s): 2 
Gene Names: PRKACA
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
UniProt
Find proteins for P00517 (Bos taurus)
Explore P00517 
Go to UniProtKB:  P00517
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00517
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor, alpha form20synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
PHAROS:  P61925
GTEx:  ENSG00000171033 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61925
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R68
Query on R68

Download Ideal Coordinates CCD File 
C [auth A]N-{4-[(4-{3-[(2R)-3,3-DIMETHYLPIPERIDIN-2-YL]-2-FLUORO-6-HYDROXYBENZOYL}BENZOYL)AMINO]AZEPAN-3-YL}ISONICOTINAMIDE
C33 H38 F N5 O4
LLDRWTNKJQFSDC-KQZWIPHESA-N
BU3
Query on BU3

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth B]
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
R68 PDBBind:  1XH5 Kd: 3400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.094α = 90
b = 76.806β = 90
c = 79.532γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-06-26
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2024-10-16
    Changes: Structure summary