3bym Summary

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X-ray co-crystal structure aminobenzimidazole triazine 1 bound to Lck

The structure was published by Martin, M.W., Newcomb, J., Nunes, J.J., et al., Ermann, M., Johnston, D., and Saluste, C.G., in 2008 in a paper entitled "Structure-based design of novel 2-amino-6-phenyl-pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-ones as potent and orally active inhibitors of lymphocyte specific kinase (Lck): synthesis, SAR, and in vivo anti-inflammatory activity." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.0 Å and deposited in 2008.

The experimental data on which the structure is based was not deposited.

The PDB entry contains the structure of Proto-oncogene tyrosine-protein kinase LCK. This molecule has the UniProt identifier P06239 (LCK_HUMAN)search. The sample contained 272 residues which is < 90% of the natural sequence. Out of 272 residues 270 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule is most likely monomeric.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Proto-oncogene tyrosine-protein kinase LCK P06239 (230-501) (LCK_HUMAN)search Homo sapienssearch < 90% 272 100%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P06239 (230 - 501) Proto-oncogene tyrosine-protein kinase LCK Homo sapiens

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A Protein kinases, catalytic subunitsearch Phosphorylase Kinase; domain 1search, Transferase(Phosphotransferase) domain 1search Protein tyrosine kinasesearch

Chain ID Biological process (GO) Molecular function (GO)
A (P06239) protein phosphorylationsearch protein tyrosine kinase activitysearch ATP bindingsearch protein kinase activitysearch transferase activity, transferring phosphorus-containing groupssearch

Chain InterPro annotation
A Protein kinase domainsearch Serine-threonine/tyrosine-protein kinase catalytic domainsearch Tyrosine-protein kinase, active sitesearch Protein kinase-like domainsearch Protein kinase, ATP binding sitesearch Tyrosine-protein kinase, catalytic domainsearch