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Table 3 Contacts observed between inhibitor 2 and N9 NA; 3LV is the residue name assigned to the inhibitor by the PDB and 488 is the residue number of the inhibitor

From: Crystal structure of a new benzoic acid inhibitor of influenza neuraminidase bound with a new tilt induced by overpacking subsite C6

Inhibitor atom

N9 atom

distance (Ã…)

Angle(D-A-AA)°

 

Potential hydrogen bonds1

3LV488-O1

Arg118-NH1

2.84

117.3

 

3LV488-O1

Arg371-NH1

2.86

112.8

 

3LV488-O2

Arg292-NH1

3.34

97.1

 

3LV488-O2

Arg292-NH2

3.25

101.2

 

3LV488-O2

Arg371-NH2

2.84

124.9

 

3LV488-O2

HOH-747

2.85

  
 

HOH-747

3.25

 

Asn347 OD1

3LV488-O15

Arg152- NH1

2.54

145.9

 

3LV488-O20

HOH-612

2.72

  
 

HOH-612

2.82, 3.16

 

Glu227 OE2, Thr225 O

Van der Waals contacts2 (≤4.0 Å)

3LV488-C1

Tyr406-OH

2.97

119.4

 
 

Arg371-NH1

3.70

96.2

 
 

Arg371-NH2

3.49

106.5

 
 

Tyr406-CZ

3.83

42.5

 

3LV488-O1

Tyr406-OH

3.50

99.8

 
 

Arg118-CZ

3.65

43.7

 
 

Arg118-NH2

3.56

83.0

 
 

Arg371-CZ

3.59

47.2

 
 

Arg371-NH2

3.45

85.5

 

3LV488-C2

Tyr406-OH

2.80

136.4

 

3LV488-O2

Tyr406-OH

3.32

123.93

 
 

Arg371-CZ

3.76

38.3

 
 

Arg371-NH1

3.82

96.2

 

3LV488-C3

Tyr406-OH

3.19

161.8

 

3LV488-C6

Glu119-OE2

3.39

119.6

 
 

Asp151-CG

3.49

74.6

 
 

Asp151-OD1

3.37

84.4

 
 

Asp151-OD2

3.87

62.7

 

3LV488-C7

Glu119-OE2

3.49

136.6

 
 

Asp151-OD1

3.52

97.7

 
 

Asp151-CG

3.89

63.8

 
 

Tyr406-OH

3.23

118.0

 
 

Arg118-NH1

3.63

113.4

 

3LV488-C10

Ile222-CD1

3.63

122.8

 

3LV488-C11

Ala246-CB

3.90

115.5

 
 

Ile222-CD1

3.54

105.5

 
 

Ile222-CB

3.88

87.6

 
 

Arg224-CZ

3.43

79.4

 
 

Arg224-NE

3.78

64.8

 
 

Arg224-NH1

3.44

78.4

 
 

Arg224-NH2

3.81

63.4

 
 

HOH-945

2.82

---

 

3LV488-C14

Arg292-NH24

3.50

140.0

 

3LV488-O15

Asp151-CB

3.59

100.5

 
 

Arg152-CG

3.84

73.6

 
 

Arg152-CD

3.71

83.0

 
 

Arg152-CZ

3.70

22.6

 

3LV488-C16

Trp178-CE3

3.59

91.2

 
 

Trp178-CZ3

3.88

67.8

 
 

Trp178-O

3.78

135.7

 
 

Arg152-CD

3.73

78.1

 
 

Arg152-CG

3.73

78.1

 

3LV488-C17

Trp178-O

3.43

139.6

 
 

Glu227-OE2

3.62

135.8

 

3LV488-C19

Trp178-O

3.19

167.7

 
 

Glu119-CD

3.88

85.8

 

3LV488-O19

Asp151-O

3.26

116.7

 
 

Asp151-CB

3.73

97.2

 
 

Arg156-NH1

3.68

139.0

 
 

Trp178-O

2.82

162.5

 

3LV488-C20

Glu227-CG

3.88

74.3

 
 

Glu227-CD

3.77

55.7

 
 

Glu227-OE2

3.23

105.4

 
 

Glu277-OE2

3.34

140.2

 

3LV488-O20

Glu227-OE2

3.68

115.2

 
 

Glu277-CG

3.80

70.4

 
 

Glu277-CD

3.59

31.9

 
 

Glu277-OE2

2.61

133.4

 

Water bridge – inhibitor – Glu276

3LV488-O20

HOH-612

2.72

  

612-HOH

553-HOH

2.64

  

553-HOH

Glu276-OE1

2.82

142.2

 

Glu276 interactions

Glu276-OE1

Arg224-NE

2.72

114.2

 

Glu276-OE2

Arg224-NE

3.50

83.2

 

Glu276-OE2

Arg224-NH2

2.81

115.9

 

Glu276-OE2

His274-NE2

2.73

119.7

 
  1. 1Potential hydrogen bonds were identified using HBPLUS[29]. Potential hydrogen bonds were interactions between donor and acceptor atoms that met the following geometric requirements: (i) a donor acceptor distance (D-A) < 3.5 Å and a hydrogen acceptor distance (H-A) < 2.5 Å and (ii) a donor-acceptor-acceptor antecedent angle (D-A-AA), of > 90° [31].
  2. 2Favorable hydrophobic contacts were defined as non-bonded contacts between two carbon atoms at a distance of ≤4 Å [28].
  3. 3Freely rotating hydroxyl hydrogen atoms had the potential to form hydrogen bonds with two alternative acceptor atoms. Only the more probable acceptor atom at the shorter distance from the hydrogen atom was reported by HBPLUS.
  4. 4There were several conformations of the propyl chain C12-C14. We used the best, but it is of low occupancy so the interactions involving C14 contribute very little.
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BMC Structural Biology

ISSN: 1472-6807

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