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Table 3 Comparisons of direct hydrogen bonding interactions between Ac-DNLD-CHO/caspase-3 and Ac-DEVD-CHO/caspase-3

From: Structural and functional definition of the specificity of a novel caspase-3 inhibitor, Ac-DNLD-CHO

Caspase-3

Ac-DNLD-CHO a

Ac-DEVD-CHO b

Active site

Residues

Atom

Residues

Atom

Distance (Ã…)

Angle (deg)

Residues

Atom

Distance (Ã…)

Angle (deg)

S4

Asn208

HD2

Asp4

OD2

3.41

174.12

Asp4

OD1

3.23

157.09

 

Trp214

HE1

Asp4

OD2

2.99

152.10

Asp4

OD1

3.78

150.54

 

Phe250

HN

Asp4

OD1

3.22

136.14

Asp4

OD2

2.76

163.40

S3

Ser209

HN

Acetyl

O

3.10

144.37

Acetyl

O

2.84

167.94

  

OG

Asn3

HD

2.69

116.54

-

-

-

-

 

Arg207

HH2

-

-

-

-

Glu3

OE2

2.87

132.63

  

O

Asn3

HN

2.82

141.89

Glu3

HN

2.77

155.73

  

HN

Asn3

O

2.80

166.06

Glu3

O

2.78

165.67

  

HH1

Leu2

O

2.93

141.53

Val2

O

3.26

141.52

S1

Arg64

HH2

Asp1

OD2

3.03

156.84

Asp1

OD1

2.72

169.65

  

HE

Asp1

OD1

2.65

128.01

Asp1

OD2

2.56

164.98

 

Ser205

O

Asp1

NH

2.66

170.78

Asp1

NH

2.84

142.41

Active site

Residues

Residues

ΔASA (Å2)c

Residues

ΔASA (Å2)c

S2

Tyr204

Leu2

145

Val2

113

 

Trp206

        
 

Phe256

        
  1. a Hydrogen bonding interactions of Ac-DNLD-CHO and caspase-3 were obtained from AutoDock docking simulations [34].
  2. bHydrogen bonding interactions of Ac-DEVD-CHO and caspase-3 were obtained from the crystal structure.
  3. cThe change in Accessible Surface Area (ASA) per Leu2 or Val2 residue upon dissociation of the complex structure was calculated by DSSP [54], and then mainly the results from the interactions with the S2 subsite. In calculating the ΔASA, it was assumed that no conformational changes in the peptide inhibitors or caspase-3 occur upon dissociation.
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BMC Pharmacology

ISSN: 1471-2210