2ZM1

Crystal structure of imidazo pyrazin 1 bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.bmc.2008.10.041
  • Primary Citation of Related Structures:  

  • 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 i ...

    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.


    Organizational Affiliation

    Kissei Pharmaceutical Company Ltd., Central Research Laboratory, 4365-1 Kashiwabara, Hotaka, Azumino, Nagano-Pref 399-8304, Japan. tomonaga_ozawa@pharm.kissei.co.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase LCK
A
285Homo sapiensMutation(s): 0 
Gene Names: LCK
EC: 2.7.10.2
Find proteins for P06239 (Homo sapiens)
Go to Gene View: LCK
Go to UniProtKB:  P06239
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KSF
Query on KSF

Download SDF File 
Download CCD File 
A
N-(2-chlorophenyl)-5-phenylimidazo[1,5-a]pyrazin-8-amine
C18 H13 Cl N4
NNBICZMPIJMWGC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KSFIC50: 220 nM (100) BINDINGDB
PTRKd: 400000 nM (100) BINDINGDB
KSFIC50: 220 nM BINDINGMOAD
KSFIC50: 220 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.308α = 90.00
b = 73.830β = 90.00
c = 92.490γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
BSSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-04-10 
  • Released Date: 2008-10-14 
  • Deposition Author(s): Tsuji, E.

Revision History 

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance