Table 3

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







a Hydrogen bonding interactions of Ac-DNLD-CHO and caspase-3 were obtained from AutoDock docking simulations [34].

bHydrogen bonding interactions of Ac-DEVD-CHO and caspase-3 were obtained from the crystal structure.

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.

Yoshimori et al. BMC Pharmacology 2007 7:8   doi:10.1186/1471-2210-7-8