3BYU

co-crystal structure of Lck and aminopyrimidine reverse amide 23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided design of aminopyrimidine amides as potent, selective inhibitors of lymphocyte specific kinase: synthesis, structure-activity relationships, and inhibition of in vivo T cell activation.

DiMauro, E.F.Newcomb, J.Nunes, J.J.Bemis, J.E.Boucher, C.Chai, L.Chaffee, S.C.Deak, H.L.Epstein, L.F.Faust, T.Gallant, P.Gore, A.Gu, Y.Henkle, B.Hsieh, F.Huang, X.Kim, J.L.Lee, J.H.Martin, M.W.McGowan, D.C.Metz, D.Mohn, D.Morgenstern, K.A.Oliveira-dos-Santos, A.Patel, V.F.Powers, D.Rose, P.E.Schneider, S.Tomlinson, S.A.Tudor, Y.Y.Turci, S.M.Welcher, A.A.Zhao, H.Zhu, L.Zhu, X.

(2008) J.Med.Chem. 51: 1681-1694

  • DOI: 10.1021/jm7010996
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The lymphocyte-specific kinase (Lck), a member of the Src family of cytoplasmic tyrosine kinases, is expressed in T cells and natural killer (NK) cells. Genetic evidence, including knockout mice and human mutations, demonstrates that Lck kinase activ ...

    The lymphocyte-specific kinase (Lck), a member of the Src family of cytoplasmic tyrosine kinases, is expressed in T cells and natural killer (NK) cells. Genetic evidence, including knockout mice and human mutations, demonstrates that Lck kinase activity is critical for normal T cell development, activation, and signaling. Selective inhibition of Lck is expected to offer a new therapy for the treatment of T-cell-mediated autoimmune and inflammatory disease. With the aid of X-ray structure-based analysis, aminopyrimidine amides 2 and 3 were designed from aminoquinazolines 1, which had previously been demonstrated to exhibit potent inhibition of Lck and T cell proliferation. In this report, we describe the synthesis and structure-activity relationships of a series of novel aminopyrimidine amides 3 possessing improved cellular potency and selectivity profiles relative to their aminoquinazoline predecessors 1. Orally bioavailable compound 13b inhibited the anti-CD3-induced production of interleukin-2 (IL-2) in mice in a dose-dependent manner (ED 50 = 9.4 mg/kg).


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Cambridge, MA 02139, USA. edimauro@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase LCK
A
277Homo sapiensMutation(s): 0 
Gene Names: LCK
EC: 2.7.10.2
Find proteins for P06239 (Homo sapiens)
Go to Gene View: LCK
Go to UniProtKB:  P06239
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AM6
Query on AM6

Download SDF File 
Download CCD File 
A
2-methyl-N-{4-methyl-3-[(2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-5-yl)carbamoyl]phenyl}-3-(trifluoromethyl)benzamide
C32 H32 F3 N7 O2
YNJXLRWECIJSPA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AM6IC50: 0.8 nM BINDINGMOAD
AM6IC50: 0.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.120α = 90.00
b = 73.720β = 90.00
c = 101.500γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
AMoREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-01-16 
  • Released Date: 2008-09-16 
  • Deposition Author(s): Huang, X.

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance