Table 2.
Molecular interactive analysis of AGP, shortlisted AGP analogs, and DNA with native NF-κB p50 protein
| Compound name | Total interacting residues | HYD bond | H-bond | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Name of residue | Distance | Analog’s interacting site | Type | Name of residue | Distance | Analog’s interacting site | Type | ||
|
DNA 5′-AGATGGGGAATCCCCTAGA-3′ |
Tyr60, Cys62, His144, Thr146, Asp209, Ser211, Tyr241, Lys244, Ala245, Pro246, Asn247, Ser338, Asp339, Leu340 | – | – | – | – | – | – | – | – |
| AGP | Tyr60, His144, Val145, Thr146, Lys147, Lys148, Leu210, Asp242, Lys244, Ala245, Pro246, Lys275 |
His144 Ala245 Pro246 Lys244 |
6.46 4.77; 5.97 4.64; 5.80 4.54; 6.95 |
2-methylidene 2-methylidene; Naphthalene 8a-methyl; 4a-8a bond 5-methyl; Naphthalene |
Alkyl |
His144, Lys244, Thr146, Lys275 |
5.04 5.90 3.94 5.52 |
2-one 5-hydroxymethyl 2-one 5-hydroxymethyl |
C-H bond H-bond C-H bond H-bond |
| Ana1 | Tyr60, His144, Leu210, Ser211, Asp242, Lys244, Ala245, Pro246, Lys275 |
Tyr60 His144 Leu210 Lys244 Ala245 Pro246 |
5.67 6.69 4.88 3.92; 5.54 4.22; 4.75; 4.90 5.21; 5.48 |
2-methylidene 10b-methyl 10b-methyl 2-methylidene; Naphthol 4a-methyl; Naphthol; 10b-methyl 4a-methyl; Naphthol |
Alkyl | Lys244 | 3.89 | 4-hydroxy | H-bond |
| Ana2 | Arg57, Tyr60, Ser243, Ala245, Pro246, Ser249, Lys244, Lys275 |
Lys244 Lys275 |
4.28; 5.04 3.62 |
Naphthol; Naphthol 8-mehylidene |
Alkyl |
Arg57 Tyr60 Lys275 |
4.23 6.28 5.53 |
4-O (dioxin) 4-hydroxy 2-one |
H-bond H bond |
| Ana3 | Tyr60, His144, Leu210, Ser211, Asp242, Lys244, Ala245, Pro246, Asn247, Lys275 |
Tyr60 His144 Leu210 Lys244 Ala245 Pro246 |
5.86 7.82 4.49 3.76 4.35; 5.03 5.58 |
2-methyl Naphthalene 5-methyl 2-methyl Naphthalene; 4a-8a bond 4a-8a bond |
Alkyl |
Lys244 Pro246 |
3.88 4.30; 4.64 |
4-hydroxy 6-fluoromethyl; 6-fluoromethyl |
H-bond C-H bond C-H bond |
| Ana4 | Arg57, Tyr60, Ser243, Lys244, Ala245, Pro246, Ser249, Asn250, Lys275 |
Pro246 Lys244 Lys275 |
4.84 5.27 4.15; 4.84; 5.16 |
2-methyl 8a-methyl 2-methyl; 8a-methyl; Naphthalene |
Alkyl |
Arg57 Tyr60 Ser243 Lys244 |
3.73 6.20 4.29 5.48 |
6-fluoromethyl 1-oxo 6-fluoromethyl 4-carbon |
H-bond H-bond H-bond C-H bond |
| Ana5 | Ser243, Lys244, Ser249, Asn250, Cys273, Asp274, Lys275, Phe310 |
Lys244 Lys275 |
4.37 3.62; 4.70; 4.98 |
5-methyl 8a-methyl; Naphthalene; 2-methyl |
Alkyl |
Asn250 Ser243 |
2.98; 3.90 3.08; 4.70 |
6-fluoromethyl; 6-hydroxy 6-hydroxy; 6-fluoromethyl |
H-bond H-bond H-bond H-bond |
HYD hydrophobic interaction, H-bond Hydrogen bond