Crystal structure of pyrimidine amide 11 bound to Lck

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

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N-(3-(phenylcarbamoyl)arylpyrimidine)-5-carboxamides as potent and selective inhibitors of Lck: structure, synthesis and SAR.

Deak, H.L.Newcomb, J.R.Nunes, J.J.Boucher, C.Cheng, A.C.DiMauro, E.F.Epstein, L.F.Gallant, P.Hodous, B.L.Huang, X.Lee, J.H.Patel, V.F.Schneider, S.Turci, S.M.Zhu, X.

(2008) Bioorg Med Chem Lett 18: 1172-1176

  • DOI: https://doi.org/10.1016/j.bmcl.2007.11.123
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    N-3-(Phenylcarbamoyl)arylpyrimidine-5-carboxamides are a novel class of selective Lck inhibitors. This series of compounds derives its selectivity from a hydrogen bond with the gatekeeper Thr316 of the enzyme. X-ray co-crystal structural data, structure-activity relationships, and the synthesis of these inhibitors are reported herein.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Building 1000, Cambridge, MA 02139, USA. holly.deak@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
PHAROS:  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 9NH

Download Ideal Coordinates CCD File 
B [auth A]N-[5-({[2-fluoro-3-(trifluoromethyl)phenyl]amino}carbonyl)-2-methylphenyl]-4-methoxy-2-[(4-piperazin-1-ylphenyl)amino]pyrimidine-5-carboxamide
C31 H29 F4 N7 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
9NH Binding MOAD:  3B2W IC50: 0.6 (nM) from 1 assay(s)
PDBBind:  3B2W IC50: 0.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.18α = 90
b = 75.19β = 112.35
c = 47.11γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2007-12-18 
  • Deposition Author(s): Huang, X.

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    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