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

Summary for 3BYM

DescriptorProto-oncogene tyrosine-protein kinase LCK, SULFATE ION, N-phenyl-1-{4-[(3,4,5-trimethoxyphenyl)amino]-1,3,5-triazin-2-yl}-1H-benzimidazol-2-amine, ... (4 entities in total)
Functional Keywordslck, kinase domain, alternative splicing, atp-binding, chromosomal rearrangement, cytoplasm, disease mutation, host-virus interaction, lipoprotein, membrane, myristate, nucleotide-binding, palmitate, phosphoprotein, proto-oncogene, sh2 domain, sh3 domain, transferase, tyrosine-protein kinase
Biological sourceHomo sapiens (human)
Cellular locationCytoplasm P06239
Total number of polymer chains1
Total molecular weight32215.62
Huang, X. (deposition date: 2008-01-16, release date: 2008-09-16, Last modification date: 2011-07-13)
Primary citation
Martin, M.W.,Newcomb, J.,Nunes, J.J.,Boucher, C.,Chai, L.,Epstein, L.F.,Faust, T.,Flores, S.,Gallant, P.,Gore, A.,Gu, Y.,Hsieh, F.,Huang, X.,Kim, J.L.,Middleton, S.,Morgenstern, K.,Oliveira-dos-Santos, A.,Patel, V.F.,Powers, D.,Rose, P.,Tudor, Y.,Turci, S.M.,Welcher, A.A.,Zack, D.,Zhao, H.,Zhu, L.,Zhu, X.,Ghiron, C.,Ermann, M.,Johnston, D.,Saluste, C.G.
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.
J.Med.Chem., 51:1637-1648, 2008
PubMed: 18278858 (PDB entries with the same primary citation)
DOI: 10.1021/jm701095m
MImport into Mendeley
Experimental method

Structure validation

ClashscoreRamachandran outliersSidechain outliers9 0.4% 0.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution
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PDB entries from 2020-10-21