Table 5 Molecular interactions with amino acids of dihydropteroate synthase of S. aureus (PDB: ID 1AD4).

Protein

Ligand

3D Structure

Hydrophilic Interactions

Hydrophobic Contacts

No. of

H-Bonds

No. of

Total Bonds

affinity

kcal mol-1

Residue (H- Bond)

Length

Residue (Bond type)

Length

1

Dihydropteroate synthase of S. aureus

Luteolin7-O-glucopyransoide

Arg204 (H- Bond)

Lys203 (H- Bond)

Arg239 (H- Bond)

Asn103 (H- Bond)

Asp84 (H- Bond)

2.16

4.73

4.70

2.64

2.04

Phe172, (Pi-Pi shaped)

Arg52, (Pi-cation)

Arg52, (Pi-cation)

Ala199, (Pi-alkyl)

Met128, (Pi-Sulfur)

Ala199, (Pi-alkyl)

4.81

4.95

3.97

4.73

3.74

2.58

5

11

−8.40

2

Myricetin 3-O-rhamnoside

Val49 (H- Bond)

Asn11 (H- Bond)

Asn11 (H- Bond)

Gln105 (H- Bond)

Lys203 (H- Bond)

Arg52 (H- Bond)

Arg202 (H- Bond)

1.91

2.97

2.60

2.44

2.57

2.53

2.46

His55, (Pi-alkyl)

Arg52, (Pi- cation)

Phe172, (Pi-Pi shaped)

4.66

4.85

4.90

7

10

−7.70

3

Quercetin 3-O-rhamnoside

Val49 (H- Bond)

Asn11 (H- Bond)

Asn11 (H- Bond)

Gln105 (H- Bond)

Arg52 (H- Bond)

Arg202 (H- Bond)

1.87

2.96

2.66

2.57

2.56

2.84

His55, (Pi-alkyl)

Arg52, (Pi-cation)

Arg52, (Pi- cation)

Phe172, (Pi-Pi shaped)

4.62

4.66

4.98

5.06

6

10

−7.40

4

Ciprofloxacin

Arg239 (H- Bond)

2.18

Ser201, (Halogen)

Arg202, (Pi-alkyl)

His241, (Pi-cation)

Lys203, (CH-bond)

Asn11, (CH-bond)

3.13

5.25

4.77

3.55

3.35

1

6

−6.10