2GU8

Discovery of 2-Pyrimidyl-5-Amidothiophenes as Novel and Potent Inhibitors for AKT: Synthesis and SAR Studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of 2-pyrimidyl-5-amidothiophenes as potent inhibitors for AKT: synthesis and SAR studies

Lin, X.Murray, J.M.Rico, A.C.Wang, M.X.Chu, D.T.Zhou, Y.Del Rosario, M.Kaufman, S.Ma, S.Fang, E.Crawford, K.Jefferson, A.B.

(2006) Bioorg Med Chem Lett 16: 4163-4168

  • DOI: 10.1016/j.bmcl.2006.05.092
  • Primary Citation of Related Structures:  
    2GU8

  • PubMed Abstract: 
  • A series of 2-pyrimidyl-5-amidothiophenes has been synthesized and evaluated for AKT inhibition. SAR studies resulted in potent inhibitors of AKT with IC(50) values as low as single digit nanomolar as represented by compound 2aa. Compound 2aa showed cellular activity including antiproliferation and downstream target modulation ...

    A series of 2-pyrimidyl-5-amidothiophenes has been synthesized and evaluated for AKT inhibition. SAR studies resulted in potent inhibitors of AKT with IC(50) values as low as single digit nanomolar as represented by compound 2aa. Compound 2aa showed cellular activity including antiproliferation and downstream target modulation. Selectivity profile is described. A co-crystal of 2aa with PKA is determined and discussed.


    Organizational Affiliation

    Small Molecule Drug Discovery, Biopharma Research, Chiron Corporation, Emeryville, CA, USA. xiaodong_lin@chiron.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAMP-dependent protein kinase, alpha-catalytic subunitA337Homo sapiensMutation(s): 0 
Gene Names: PRKACAPKACA
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens)
Explore P17612 
Go to UniProtKB:  P17612
PHAROS:  P17612
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
inhibitor of CAMP-dependent protein kinaseB [auth C]20N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
796 (Subject of Investigation/LOI)
Query on 796

Download Ideal Coordinates CCD File 
C [auth A]N-[(1S)-2-AMINO-1-(2,4-DICHLOROBENZYL)ETHYL]-5-[2-(METHYLAMINO)PYRIMIDIN-4-YL]THIOPHENE-2-CARBOXAMIDE
C19 H19 Cl2 N5 O S
HHOVRZGUSBMKKU-ZDUSSCGKSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
796 BindingDB:  2GU8 IC50: 0.1 (nM) from 1 assay(s)
PDBBind:  2GU8 IC50: 2.6 (nM) from 1 assay(s)
Binding MOAD:  2GU8 IC50: 0.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.72α = 90
b = 75.165β = 90
c = 79.844γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2006-04-28 
  • Released Date: 2007-05-01 
  • Deposition Author(s): Murray, J.M.

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance