2HK5

Hck Kinase in Complex with Lck targetted Inhibitor PG-1009247

• PDB DOI: https://doi.org/10.2210/pdb2HK5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-03 Released: 2006-09-05 
• Deposition Author(s): Walter, R.L., Mekel, M.J., Evdokimov, A.G., Pokross, M.E., Sabat, M.P.

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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

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

• PubMed: 16997556 
• 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).

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Organizational Affiliation: 

Procter and Gamble Pharmaceuticals, Health Care Research Center, 8700 Mason-Montgomery Rd., Mason, OH 45040, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.4 kDa 
• Atom Count: 2,429 
• Modelled Residue Count: 269 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase HCK	A	270	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1BM	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
ID	Source	Binding 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 = 96.977	α = 90
b = 96.977	β = 90
c = 69.998	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-05 
Deposition Author(s): Walter, R.L., Mekel, M.J., Evdokimov, A.G., Pokross, M.E., Sabat, M.P.

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