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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 compoundHydrogen bonds < 3 Åvan der Waals interactionsπ-π
Residue atomLigand atomBond length
Co-crystalLeu83: 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
ReferenceGlu12: 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
HitLeu83: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, Val164Ile10, Val18, Leu134, Leu298