3MV5

Crystal structure of Akt-1-inhibitor complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design of selective, ATP-competitive inhibitors of Akt.

Freeman-Cook, K.D.Autry, C.Borzillo, G.Gordon, D.Barbacci-Tobin, E.Bernardo, V.Briere, D.Clark, T.Corbett, M.Jakubczak, J.Kakar, S.Knauth, E.Lippa, B.Luzzio, M.J.Mansour, M.Martinelli, G.Marx, M.Nelson, K.Pandit, J.Rajamohan, F.Robinson, S.Subramanyam, C.Wei, L.Wythes, M.Morris, J.

(2010) J Med Chem 53: 4615-4622

  • DOI: 10.1021/jm1003842
  • Primary Citation of Related Structures:  
    3MV5, 3MVH, 3MVJ

  • PubMed Abstract: 
  • This paper describes the design and synthesis of novel, ATP-competitive Akt inhibitors from an elaborated 3-aminopyrrolidine scaffold. Key findings include the discovery of an initial lead that was modestly selective and medicinal chemistry optimizat ...

    This paper describes the design and synthesis of novel, ATP-competitive Akt inhibitors from an elaborated 3-aminopyrrolidine scaffold. Key findings include the discovery of an initial lead that was modestly selective and medicinal chemistry optimization of that lead to provide more selective analogues. Analysis of the data suggested that highly lipophilic analogues would likely suffer from poor overall properties. Central to the discussion is the concept of optimization of lipophilic efficiency and the ability to balance overall druglike propeties with the careful control of lipophilicity in the lead series. Discovery of the nonracemic amide series and subsequent modification produced an advanced analogue that performed well in advanced preclinical assays, including xenograft tumor growth inhibition studies, and this analogue was nominated for clinical development.


    Organizational Affiliation

    Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, USA. kevin.freeman-cook@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
v-akt murine thymoma viral oncogene homolog 1 (AKT1)A342Homo sapiensMutation(s): 1 
Gene Names: AKT-1AKT1PKBRAC
EC: 2.7.11.1
Find proteins for P31749 (Homo sapiens)
Explore P31749 
Go to UniProtKB:  P31749
NIH Common Fund Data Resources
PHAROS  P31749
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GSK3-beta peptideC10N/AMutation(s): 0 
Find proteins for P49841 (Homo sapiens)
Explore P49841 
Go to UniProtKB:  P49841
NIH Common Fund Data Resources
PHAROS  P49841
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XFE
Query on XFE

Download CCD File 
A
(3R)-1-(5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrrolidin-3-amine
C11 H15 N5
SMTIKTZYKPWXQP-MRVPVSSYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 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 %)
XFEIC50 :  180   nM  PDBBind
XFEIC50:  180   nM  Binding MOAD
XFEIC50:  180   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.706α = 90
b = 55.417β = 104
c = 93.287γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-05-03 
  • Released Date: 2010-06-02 
  • Deposition Author(s): Pandit, J.

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance