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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 (Å) Angle (deg) Residues Atom Distance (Å) 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.