3L9L

Crystal structure of pka with compound 36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 ...

    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:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor alphaCD20Homo sapiensMutation(s): 0 
Gene Names: PKIAPRKACN1
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
NIH Common Fund Data Resources
PHAROS  P61925
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaAB351Homo sapiensMutation(s): 0 
Gene Names: PRKACAPKACA
EC: 2.7.11.11
Find proteins for P17612 (Homo sapiens)
Explore P17612 
Go to UniProtKB:  P17612
NIH Common Fund Data Resources
PHAROS  P17612
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L9L
Query on L9L

Download CCD File 
A, B
5-[2-({(2S)-2-amino-3-[4-(trifluoromethyl)phenyl]propyl}amino)-1,3-thiazol-5-yl]-1,3-dihydro-2H-indol-2-one
C21 H19 F3 N4 O S
XPPKIHZJFAAJLB-INIZCTEOSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A,BL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A,BL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L9LIC50:  167   nM  Binding MOAD
L9LIC50 :  167   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.039α = 90
b = 114.424β = 125.786
c = 71.807γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-16
    Changes: Atomic model