3L9N

crystal structure of PKAB3 (pka triple mutant V123A, L173M, Q181K) with compound 27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Azole-based inhibitors of AKT/PKB for the treatment of cancer.

Zeng, Q.Allen, J.G.Bourbeau, M.P.Wang, X.Yao, G.Tadesse, S.Rider, J.T.Yuan, C.C.Hong, F.T.Lee, M.R.Zhang, S.Lofgren, J.A.Freeman, D.J.Yang, S.Li, C.Tominey, E.Huang, X.Hoffman, D.Yamane, H.K.Fotsch, C.Dominguez, C.Hungate, R.Zhang, X.

(2010) Bioorg Med Chem Lett 20: 1559-1564

  • DOI: 10.1016/j.bmcl.2010.01.067
  • Primary Citation of Related Structures:  
    3L9L, 3L9M, 3L9N

  • PubMed Abstract: 
  • Through a combination of screening and structure-based rational design, we have discovered a series of N(1)-(5-(heterocyclyl)-thiazol-2-yl)-3-(4-trifluoromethylphenyl)-1,2-propanediamines that were developed into potent ATP competitive inhibitors of AKT. Studies of linker strand-binding adenine isosteres identified SAR trends in potency and selectivity that were consistent with binding interactions observed in structures of the inhibitors bound to AKT1 and to the counter-screening target PKA ...

    Through a combination of screening and structure-based rational design, we have discovered a series of N(1)-(5-(heterocyclyl)-thiazol-2-yl)-3-(4-trifluoromethylphenyl)-1,2-propanediamines that were developed into potent ATP competitive inhibitors of AKT. Studies of linker strand-binding adenine isosteres identified SAR trends in potency and selectivity that were consistent with binding interactions observed in structures of the inhibitors bound to AKT1 and to the counter-screening target PKA. One compound was shown to have acceptable pharmacokinetic properties and to be a potent inhibitor of AKT signaling and of in vivo xenograft tumor growth in a preclinical model of glioblastoma.


    Organizational Affiliation

    Chemistry Research and Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaA351Homo sapiensMutation(s): 3 
Gene Names: PRKACAPKACA
EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens)
Explore P17612 
Go to UniProtKB:  P17612
PHAROS:  P17612
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor alphaB [auth C]20Homo sapiensMutation(s): 0 
Gene Names: PKIAPRKACN1
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
PHAROS:  P61925
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L9N (Subject of Investigation/LOI)
Query on L9N

Download Ideal Coordinates CCD File 
C [auth A](2S)-N~1~-[5-(1H-indazol-5-yl)-1,3,4-thiadiazol-2-yl]-3-(4-methylphenyl)propane-1,2-diamine
C19 H20 N6 S
XFEMJTFDPFGXFN-INIZCTEOSA-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
L9N PDBBind:  3L9N IC50: 8.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.217 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.02α = 90
b = 118.32β = 90
c = 110.38γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2010-01-05 
  • Released Date: 2011-01-19 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance