3B2W

Crystal structure of pyrimidine amide 11 bound to Lck


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1016/j.bmcl.2007.11.123
  • Primary Citation of Related Structures:  
    3B2W

  • 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, struct ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase LCKA277Homo sapiensMutation(s): 0 
Gene Names: LCK
EC: 2.7.10.2
Find proteins for P06239 (Homo sapiens)
Explore P06239 
Go to UniProtKB:  P06239
NIH Common Fund Data Resources
PHAROS  P06239
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9NH
Query on 9NH

Download CCD File 
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
RZSXAGWVTKQZAS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9NHIC50:  0.6000000238418579   nM  Binding MOAD
9NHIC50 :  0.6000000238418579   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-10-19 
  • Released Date: 2007-12-18 
  • Deposition Author(s): Huang, X.

Revision History 

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance