3CQW

Crystal Structure of Akt-1 complexed with substrate peptide and inhibitor

  • Classification: TRANSFERASE
  • Mutation(s): Yes 

  • Deposited: 2008-04-03 Released: 2008-05-27 
  • Deposition Author(s): Pandit, J.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Synthesis and structure based optimization of novel Akt inhibitors

Lippa, B.Pan, G.Corbett, M.Li, C.Kauffman, G.S.Pandit, J.Robinson, S.Wei, L.Kozina, E.Marr, E.S.Borzillo, G.Knauth, E.Barbacci-Tobin, E.G.Vincent, P.Troutman, M.Baker, D.Rajamohan, F.Kakar, S.Clark, T.Morris, J.

(2008) Bioorg Med Chem Lett 18: 3359-3363

  • DOI: 10.1016/j.bmcl.2008.04.034
  • Primary Citation of Related Structures:  
    3CQU, 3CQW

  • PubMed Abstract: 
  • Based on a high throughput screening hit, pyrrolopyrimidine inhibitors of the Akt kinase are explored. X-ray co-crystal structures of two lead series results in the understanding of key binding interactions, the design of new lead series, and enhance ...

    Based on a high throughput screening hit, pyrrolopyrimidine inhibitors of the Akt kinase are explored. X-ray co-crystal structures of two lead series results in the understanding of key binding interactions, the design of new lead series, and enhanced potency. The syntheses of these series and their biological activities are described. Spiroindoline 13j is found to have an Akt1 kinase IC(50) of 2.4+/-0.6 nM, Akt cell potency of 50+/-19 nM, and provides 68% inhibition of tumor growth in a mouse xenograft model (50 mg/kg, qd, po).


    Organizational Affiliation

    Pfizer, Inc., PGRD Groton, 558 Eastern Point Road, Groton, CT 06340, USA. blaise.lippa@cubist.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAC-alpha serine/threonine-protein kinaseA342N/AMutation(s): 2 
Gene Names: AKT1PKBRAC
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
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 betaC10N/AMutation(s): 0 
EC: 2.7.11.26
Find proteins for P49841 (Homo sapiens)
Explore P49841 
Go to UniProtKB:  P49841
NIH Common Fund Data Resources
PHAROS  P49841
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CQW
Query on CQW

Download CCD File 
A
5-(5-chloro-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridine
C12 H11 Cl N6
YFFJXGRXFASBDL-UHFFFAOYSA-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 %)
CQWIC50 :  42   nM  PDBBind
CQWIC50:  42   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.505α = 90
b = 55.879β = 102.36
c = 92.864γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-04-03 
  • Released Date: 2008-05-27 
  • Deposition Author(s): Pandit, J.

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance