2VNW

Structure of PKA-PKB chimera complexed with (1-(9H-Purin-6-yl) piperidin-4-yl)methanamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.247 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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Literature

Identification of 4-(4-Aminopiperidin-1-Yl)-7H-Pyrrolo[2,3-D]Pyrimidines as Selective Inhibitors of Protein Kinase B Through Fragment Elaboration.

Caldwell, J.J.Davies, T.G.Donald, A.Mchardy, T.Rowlands, M.G.Aherne, G.W.Hunter, L.K.Taylor, K.Ruddle, R.Raynaud, F.I.Verdonk, M.Workman, P.Garrett, M.D.Collins, I.

(2008) J Med Chem 51: 2147

  • DOI: https://doi.org/10.1021/jm701437d
  • Primary Citation of Related Structures:  
    2VNW, 2VNY, 2VO0, 2VO3, 2VO6, 2VO7

  • PubMed Abstract: 

    Fragment-based screening identified 7-azaindole as a protein kinase B inhibitor scaffold. Fragment elaboration using iterative crystallography of inhibitor-PKA-PKB chimera complexes efficiently guided improvements in the potency and selectivity of the compounds, resulting in the identification of nanomolar 6-(piperidin-1-yl)purine, 4-(piperidin-1-yl)-7-azaindole, and 4-(piperidin-1-yl)pyrrolo[2,3- d]pyrimidine inhibitors of PKBbeta with antiproliferative activity and showing pathway inhibition in cells. A divergence in the binding mode was seen between 4-aminomethylpiperidine and 4-aminopiperidine containing molecules. Selectivity for PKB vs PKA was observed with 4-aminopiperidine derivatives, and the most PKB-selective inhibitor (30-fold) showed significantly different bound conformations between PKA and PKA-PKB chimera.


  • Organizational Affiliation

    Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT351Bos taurusMutation(s): 4 
EC: 2.7.11.11
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 ALPHAB [auth I]20Homo sapiensMutation(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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M01
Query on M01

Download Ideal Coordinates CCD File 
C [auth A]1-[1-(9H-purin-6-yl)piperidin-4-yl]methanamine
C11 H16 N6
ZUPAKXAQBFFNRP-UHFFFAOYSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.247 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.84α = 90
b = 74.545β = 90
c = 79.932γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted M01Click on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary