3OCB

Akt1 kinase domain with pyrrolopyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of pyrrolopyrimidine inhibitors of Akt.

Blake, J.F.Kallan, N.C.Xiao, D.Xu, R.Bencsik, J.R.Skelton, N.J.Spencer, K.L.Mitchell, I.S.Woessner, R.D.Gloor, S.L.Risom, T.Gross, S.D.Martinson, M.Morales, T.H.Vigers, G.P.Brandhuber, B.J.

(2010) Bioorg Med Chem Lett 20: 5607-5612

  • DOI: 10.1016/j.bmcl.2010.08.053
  • Primary Citation of Related Structures:  
    3OCB

  • PubMed Abstract: 
  • The discovery and optimization of a series of pyrrolopyrimidine based protein kinase B (Pkb/Akt) inhibitors discovered via HTS and structure based drug design is reported. The compounds demonstrate potent inhibition of all three Akt isoforms and knockdown of phospho-PRAS40 levels in LNCaP cells and tumor xenografts ...

    The discovery and optimization of a series of pyrrolopyrimidine based protein kinase B (Pkb/Akt) inhibitors discovered via HTS and structure based drug design is reported. The compounds demonstrate potent inhibition of all three Akt isoforms and knockdown of phospho-PRAS40 levels in LNCaP cells and tumor xenografts.


    Organizational Affiliation

    Array BioPharma Inc, 3200 Walnut Street, Boulder, CO 80301, USA. jblake@arraybiopharma.com



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
v-akt murine thymoma viral oncogene homolog 1 (AKT1)A, B341Homo sapiensMutation(s): 1 
Gene Names: AKT1PKBRAC
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P31749 (Homo sapiens)
Explore P31749 
Go to UniProtKB:  P31749
PHAROS:  P31749
GTEx:  ENSG00000142208 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31749
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GSK 3 beta peptideC, D10N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XM1
Query on XM1

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
(2S)-2-(4-chlorobenzyl)-3-oxo-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazin-1-yl]propan-1-amine
C20 H23 Cl N6 O
IYQSFRNHWXBIKV-HNNXBMFYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, B L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
XM1 PDBBind:  3OCB IC50: 5 (nM) from 1 assay(s)
BindingDB:  3OCB IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.265α = 90
b = 56.013β = 104.27
c = 91.65γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance