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 3BYU | pdb_00003byu

co-crystal structure of Lck and aminopyrimidine reverse amide 23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.278 (Depositor) 
  • R-Value Work: 
    0.232 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3BYU

This is version 1.2 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: https://doi.org/10.1021/jm7010996
  • Primary Citation 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

Macromolecule Content 

  • Total Structure Weight: 32.66 kDa 
  • Atom Count: 2,239 
  • Modeled Residue Count: 256 
  • Deposited Residue Count: 277 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase LCK277Homo sapiensMutation(s): 0 
Gene Names: LCK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06239 (Homo sapiens)
Explore P06239 
Go to UniProtKB:  P06239
PHAROS:  P06239
GTEx:  ENSG00000182866 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06239
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AM6

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
YNJXLRWECIJSPA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AM6 BindingDB:  3BYU IC50: 0.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.278 (Depositor) 
  • R-Value Work:  0.232 (Depositor) 
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
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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