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PDBsum entry 2zm4
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protein ligands links
Transferase PDB id
2zm4

 

 

 

 

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Contents
Protein chain
271 a.a. *
Ligands
SO4 ×2
DMS
KSM
Waters ×103
* Residue conservation analysis
PDB id:
2zm4
Name: Transferase
Title: Crystal structure of imidazo quinoxaline 1 bound to the kinase domain of human lck, activated form (auto-phosphorylated on tyr394)
Structure: Proto-oncogene tyrosine-protein kinase lck. Chain: a. Fragment: unp residues 225-509. Synonym: p56-lck, lymphocyte cell-specific protein-tyrosine kinase, lsk, t cell-specific protein-tyrosine kinase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: lck. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
Resolution:
2.70Å     R-factor:   0.186     R-free:   0.274
Authors: E.Tsuji
Key ref: T.Ozawa et al. (2008). 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. Bioorg Med Chem Lett, 16, 10311-10318. PubMed id: 18977146
Date:
11-Apr-08     Release date:   14-Oct-08    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06239  (LCK_HUMAN) -  Tyrosine-protein kinase Lck from Homo sapiens
Seq:
Struc: 		509 a.a.
271 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.10.2  - non-specific protein-tyrosine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H+
L-tyrosyl-[protein]
 + ATP
 = O-phospho-L-tyrosyl-[protein]
 + ADP
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Bioorg Med Chem Lett 16:10311-10318 (2008)
PubMed id: 18977146  
 
 
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.
T.Ozawa, E.Tsuji, M.Ozawa, C.Handa, H.Mukaiyama, T.Nishimura, S.Kobayashi, K.Okazaki.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20490879 J.P.Yesudas, F.B.Sayyed, and C.H.Suresh (2011).
Analysis of structural water and CH···π interactions in HIV-1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT.
  J Mol Model, 17, 401-413.  
19603964 T.Nagata, D.G.Fedorov, K.Kitaura, and M.S.Gordon (2009).
A combined effective fragment potential-fragment molecular orbital method. I. The energy expression and initial applications.
  J Chem Phys, 131, 024101.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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