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Table 6 Intermolecular interaction between the protein and the ligands

From: Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Name of the compound Hydrogen bonds < 3 Å van der Waals interactions π-π
Residue atom Ligand atom Bond length
Co-crystal Leu83: O Leu83:HN Asp86:HN Lys89:HZ2 Lys89:HZ3 H42 N20 O31 O32 O32 2.2 2.0 2.5 2.4 2.4 Gly11, Glu12, Lys20, Lys33, Val64, Glu81, Gln85, Lys88, Gln131, Asn132, Leu148, Val18, Ala31, Phe80, Phe82, Leu134, Ala144
Reference Glu12: O Gly16:HN Lys89:HZ2 Lys89:HZ2 Lys89:HZ3 H43 O27 O34 O31 O29 3.0 2.2 2.3 1.9 2.5 Gly11, Tyr15, Val18, Gln85, Asp86, Asp127, Lys129, Gln131, Asn132, Leu134, Leu298, Phe82
Hit Leu83:HN Lys89:HZ2 Gln131: O O25 O24 H36 2.1 2.4 2.2 Gly11, Glu12, Ala31, Lys33, Val64, Phe82, His84, Gln85, Asp86, Lys129, Asn132, Asp145, Ala144, Val164 Ile10, Val18, Leu134, Leu298