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 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
v-akt murine thymoma viral oncogene homolog 1 (AKT1)
A
342Homo sapiensMutation(s): 1 
Gene Names: AKT1 (PKB, RAC)
EC: 2.7.11.1
Find proteins for P31749 (Homo sapiens)
Go to Gene View: AKT1
Go to UniProtKB:  P31749
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GSK3-beta peptide
C
10Homo sapiensMutation(s): 0 
Gene Names: GSK3B
EC: 2.7.11.26
Find proteins for P49841 (Homo sapiens)
Go to Gene View: GSK3B
Go to UniProtKB:  P49841
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
XFE
Query on XFE

Download SDF File 
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XFEIC50: 180 nM (99) BINDINGDB
XFEIC50: 180 nM BINDINGMOAD
XFEIC50: 180 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.706α = 90.00
b = 55.417β = 104.00
c = 93.287γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
CrystalCleardata collection
PDB_EXTRACTdata extraction
REFMACrefinement
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance