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 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/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 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. [email protected]


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase HCK270Homo sapiensMutation(s): 0 
Gene Names: HCK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P08631 (Homo sapiens)
Explore P08631 
Go to UniProtKB:  P08631
PHAROS:  P08631
GTEx:  ENSG00000101336 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08631
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1BM
Query on 1BM
Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
1BM BindingDB:  2HK5 IC50: 46 (nM) from 1 assay(s)
PDBBind:  2HK5 IC50: 46 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.6: 2024-04-03
    Changes: Refinement description