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: 2.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/10.1021/jm701095m
  • Primary Citation of Related Structures:  
    3BYM, 3BYO

  • 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-mediated signaling, leading to normal T-cell development and activation ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase LCKA271Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06239
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AM9
Query on AM9
Download Ideal Coordinates CCD File 
C [auth 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 Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
PTR BindingDB:  3BYO Kd: 4.00e+5 (nM) from 1 assay(s)
AM9 Binding MOAD:  3BYO IC50: 7 (nM) from 1 assay(s)
BindingDB:  3BYO IC50: min: 7, max: 1600 (nM) from 2 assay(s)
PDBBind:  3BYO IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 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
b = 73.544β = 90
c = 92.668γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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