co-crystal structure of Lck and aminopyrimidine reverse amide 23

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.232 

Starting Model: experimental
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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: https://doi.org/10.1021/jm7010996
  • Primary Citation of Related Structures:  
    3BYS, 3BYU

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase LCK277Homo sapiensMutation(s): 0 
Gene Names: LCK
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens)
Explore P06239 
Go to UniProtKB:  P06239
GTEx:  ENSG00000182866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06239
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AM6

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
AM6 BindingDB:  3BYU IC50: 0.8 (nM) from 1 assay(s)
PDBBind:  3BYU IC50: 0.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.12α = 90
b = 73.72β = 90
c = 101.5γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description