3BYO

X-Ray co-crystal structure of 2-amino-6-phenylpyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-one 25 bound to Lck


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based design of novel 2-amino-6-phenyl-pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-ones as potent and orally active inhibitors of lymphocyte specific kinase (Lck): synthesis, SAR, and in vivo anti-inflammatory activity.

Martin, M.W.Newcomb, J.Nunes, J.J.Boucher, C.Chai, L.Epstein, L.F.Faust, T.Flores, S.Gallant, P.Gore, A.Gu, Y.Hsieh, F.Huang, X.Kim, J.L.Middleton, S.Morgenstern, K.Oliveira-dos-Santos, A.Patel, V.F.Powers, D.Rose, P.Tudor, Y.Turci, S.M.Welcher, A.A.Zack, D.Zhao, H.Zhu, L.Zhu, X.Ghiron, C.Ermann, M.Johnston, D.Saluste, C.G.

(2008) J.Med.Chem. 51: 1637-1648

  • DOI: 10.1021/jm701095m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lck, or lymphocyte specific kinase, is a cytoplasmic tyrosine kinase of the Src family expressed in T-cells and NK cells. Genetic evidence from knockout mice and human mutations demonstrates that Lck kinase activity is critical for T-cell receptor-me ...

    Lck, or lymphocyte specific kinase, is a cytoplasmic tyrosine kinase of the Src family expressed in T-cells and NK cells. Genetic evidence from knockout mice and human mutations demonstrates that Lck kinase activity is critical for T-cell receptor-mediated signaling, leading 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 structure-guided design, synthesis, structure-activity relationships, and pharmacological characterization of 2-amino-6-phenylpyrimido[5',4':5,6]pyrimido[1,2- a]benzimidazol-5(6 H)-ones, a new class of compounds that are potent inhibitors of Lck. The most promising compound of this series, 6-(2,6-dimethylphenyl)-2-((4-(4-methyl-1-piperazinyl)phenyl)amino)pyrimido[5',4':5,6]pyrimido-[1,2- a]benzimidazol-5(6 H)-one ( 25), exhibits potent inhibition of Lck kinase activity. This activity translates into inhibition of in vitro cell-based assays and in vivo models of T-cell activation and arthritis, respectively.


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Kendall Square, Cambridge, MA 02139, USA. matmarti@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase LCK
A
271Homo sapiensMutation(s): 0 
Gene 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
AM9
Query on AM9

Download SDF File 
Download CCD File 
A
6-(2,6-dimethylphenyl)-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-one
C31 H30 N8 O
BHJJWVDKNXABFS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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 %)
AM9IC50: 7 nM BINDINGMOAD
AM9IC50: 7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.134α = 90.00
b = 73.544β = 90.00
c = 92.668γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-01-16 
  • Released Date: 2008-12-30 
  • Deposition Author(s): Huang, X.

Revision History 

  • Version 1.0: 2008-12-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance