Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.48 kDa 
• Atom Count: 2,435 
• Modelled Residue Count: 271 
• Deposited Residue Count: 285 
• Unique protein chains: 1

 2ZYB

Crystal structure of phenylimidazo pyrazin 2 bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)

• PDB DOI:  https://doi.org/10.2210/pdb2ZYB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-01-19 Released: 2009-02-03 
• Deposition Author(s): Tsuji, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.291 
• R-Value Work: 0.171 
• R-Value Observed: 0.183 

Literature

The importance of CH/pi hydrogen bonds in rational drug design: An ab initio fragment molecular orbital study to leukocyte-specific protein tyrosine (LCK) kinase

Ozawa, T., Tsuji, E., Ozawa, M., Handa, C., Mukaiyama, H., Nishimura, T., Kobayashi, S., Okazaki, K.

(2008) Bioorg Med Chem 16: 10311-10318

• PubMed: 18977146 
• DOI: https://doi.org/10.1016/j.bmc.2008.10.041
• Primary Citation of Related Structures:  
  2ZM1, 2ZM4, 2ZYB


• PubMed Abstract: 
  

The interaction energy was calculated, by the ab initio FMO method, for complexes between LCK protein and four inhibitors (staurosporine, BMS compound 2, and our compounds 3 and 4). In every case a number of CH/pi hydrogen bonds have been disclosed in the so-called adenine pocket. In complexes of 2, 3, and 4, CH/pi and NH/pi hydrogen bonds have been observed in another pocket. In view of the above results, the aniline ring of 3 was replaced by 2,6-dimethyl aniline to increase the potency for LCK kinase. A 10-fold increase in the potency has been achieved for 4 over 3. We suggest that the concept of weak hydrogen bonds is useful in the rational design of drugs.

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Organizational Affiliation: 

Kissei Pharmaceutical Company Ltd., Central Research Laboratory, 4365-1 Kashiwabara, Hotaka, Azumino, Nagano-Pref 399-8304, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase LCK	A	285	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KSL	C [auth A]	N-(2,6-dimethylphenyl)-5-phenylimidazo[1,5-a]pyrazin-8-amine C20 H18 N4 KKYYLKPGILUPOA-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
PTR	BindingDB:  2ZYB	Kd: 4.00e+5 (nM) from 1 assay(s)
KSL	PDBBind:  2ZYB	IC50: 20 (nM) from 1 assay(s)
	BindingDB:  2ZYB	IC50: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.291 
• R-Value Work: 0.171 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.15	α = 90
b = 73.973	β = 90
c = 92.857	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BSS	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Tsuji, E.

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance