2OFU

x-ray crystal structure of 2-aminopyrimidine carbamate 43 bound to Lck


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel 2-Aminopyrimidine Carbamates as Potent and Orally Active Inhibitors of Lck: Synthesis, SAR, and in Vivo Antiinflammatory Activity

Martin, M.W.Newcomb, J.Nunes, J.J.McGowan, D.C.Armistead, D.M.Boucher, C.Buchanan, J.L.Buckner, W.Chai, L.Elbaum, D.Epstein, L.F.Faust, T.Flynn, S.Gallant, P.Gore, A.Gu, Y.Hsieh, F.Huang, X.Lee, J.H.Metz, D.Middleton, S.Mohn, D.Morgenstern, K.Morrison, M.J.Novak, P.M.Oliveira-dos-Santos, A.Powers, D.Rose, P.Schneider, S.Sell, S.Tudor, Y.Turci, S.M.Welcher, A.A.White, R.D.Zack, D.Zhao, H.Zhu, L.Zhu, X.Ghiron, C.Amouzegh, P.Ermann, M.Jenkins, J.Johnston, D.Napier, S.Power, E.

(2006) J.Med.Chem. 49: 4981

  • DOI: 10.1021/jm060435i

  • PubMed Abstract: 
  • The lymphocyte-specific kinase (Lck) is a cytoplasmic tyrosine kinase of the Src family expressed in T cells and NK cells. Genetic evidence in both mice and humans demonstrates that Lck kinase activity is critical for signaling mediated by the T cell ...

    The lymphocyte-specific kinase (Lck) is a cytoplasmic tyrosine kinase of the Src family expressed in T cells and NK cells. Genetic evidence in both mice and humans demonstrates that Lck kinase activity is critical for signaling mediated by the T cell receptor (TCR), which leads to normal T cell development and activation. A small molecule inhibitor of Lck is expected to be useful in the treatment of T cell-mediated autoimmune and inflammatory disorders and/or organ transplant rejection. In this paper, we describe the synthesis, structure-activity relationships, and pharmacological characterization of 2-aminopyrimidine carbamates, a new class of compounds with potent and selective inhibition of Lck. The most promising compound of this series, 2,6-dimethylphenyl 2-((3,5-bis(methyloxy)-4-((3-(4-methyl-1-piperazinyl)propyl)oxy)phenyl)amino)-4-pyrimidinyl(2,4-bis(methyloxy)phenyl)carbamate (43) exhibits good activity when evaluated in in vitro assays and in an in vivo model of T cell activation.


    Organizational Affiliation

    Department of Chemistry Research and Discovery, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, USA. matmarti@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase LCK
A
273Homo sapiensGene 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
1N9
Query on 1N9

Download SDF File 
Download CCD File 
A
2,6-DIMETHYLPHENYL 2-(3,5-DIMETHOXY-4-(3-(4-METHYLPIPERAZIN-1-YL)PROPOXY)PHENYLAMINO)PYRIMIDIN- 4-YL(2,4-DIMETHOXYPHENYL)CARBAMATE
C37 H46 N6 O7
VSJXTUFWPAOYLC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PTRKd: 400000 nM (100) BINDINGDB
1N9IC50: 0.6 nM (100) BINDINGDB
1N9IC50: ~3000 nM BINDINGMOAD
1N9IC50: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.430α = 90.00
b = 73.530β = 90.00
c = 92.810γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CrystalCleardata collection
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-01-04 
  • Released Date: 2007-02-27 
  • Deposition Author(s): Huang, X.

Revision History 

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance