2HK5

Hck Kinase in Complex with Lck targetted Inhibitor PG-1009247


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The development of 2-benzimidazole substituted pyrimidine based inhibitors of lymphocyte specific kinase (Lck).

Sabat, M.VanRens, J.C.Laufersweiler, M.J.Brugel, T.A.Maier, J.Golebiowski, A.De, B.Easwaran, V.Hsieh, L.C.Walter, R.L.Mekel, M.J.Evdokimov, A.Janusz, M.J.

(2006) Bioorg Med Chem Lett 16: 5973-5977

  • DOI: 10.1016/j.bmcl.2006.08.132
  • Primary Citation of Related Structures:  
    2HK5

  • PubMed Abstract: 
  • This communication details the synthesis, biological activity, and binding mode of a novel class of 2-benzimidazole substituted pyrimidines. The most potent analogs disclosed showed low nanomolar activity for the inhibition of Lck kinase and a repres ...

    This communication details the synthesis, biological activity, and binding mode of a novel class of 2-benzimidazole substituted pyrimidines. The most potent analogs disclosed showed low nanomolar activity for the inhibition of Lck kinase and a representative analog was co-crystallized with Hck (a structurally related member of the Src family kinases).


    Organizational Affiliation

    Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Rd., Mason, OH 45040, USA. Mark.Sabat@Takedasd.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase HCKA270Homo sapiensMutation(s): 0 
Gene Names: HCK
EC: 2.7.10.2
Find proteins for P08631 (Homo sapiens)
Explore P08631 
Go to UniProtKB:  P08631
NIH Common Fund Data Resources
PHAROS  P08631
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1BM
Query on 1BM

Download CCD File 
A
3-{[2-(1H-BENZIMIDAZOL-1-YL)-6-{[2-(DIETHYLAMINO)ETHYL]AMINO}PYRIMIDIN-4-YL]AMINO}-4-METHYLPHENOL
C24 H29 N7 O
OAILDJYOGMMAOQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1BMIC50:  46   nM  BindingDB
1BMIC50:  46   nM  Binding MOAD
1BMIC50 :  46   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.977α = 90
b = 96.977β = 90
c = 69.998γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2015-04-15
    Changes: Database references
  • Version 1.4: 2017-10-18
    Changes: Refinement description