Table 6 Affinities of polygonumins A and pepstatin docked in HIV-1 protease mutants. Residues of HIV-1 protease mutants involved in hydrogen bond interactions with polygonumins A and pepstatin.
Protease Mutant (PDB ID) | Affinity (kcal/mol) | Residues involved in hydrogen bond interaction with ligand : hydrogen bond distance | ||
|---|---|---|---|---|
Polygonumins A | Pepstatin | Polygonumins A | Pepstatin | |
3KT5 | −7.3 | −8.5 | ASP 1029: 3.038 LYS 1045: 2.937 ASP 1030: 3.459 | ASP 29: 3.103 GLY 1027: 3.315 GLY 48: 3.244 |
3NU4 | −8.3 | −8.6 | ASP 29: 3.346 LYS 45: 2.912 LYS 45: 3.176 | ASP 29: 2.761 GLY 27: 3.139 GLY 27: 2.985 GLY 127: 3.243 |
3NU5 | −9.1 | −8.3 | LYS 145: 3.386 LYS 145: 2.800 GLY 148: 3.285 GLU 21: 3.345 | VAL 50: 3.225 VAL 150: 3.171 GLY 48: 2.972 ASP 29: 2.859 |
3NU6 | −8.3 | −8.3 | LYS 45: 3.126 ARG 87: 3.111 ARG 87: 3.039 ARG 8: 2.982 ARG 8: 3.257 ARG 8: 3.335 ARG 8: 3.211 | ARG 8: 3.099 ARG 8: 3.006 ASP 29: 3.269 GLY 27: 2.957 GLY 48: 3.089 GLY 27: 2.779 |
3NU9 | −9.3 | −8.3 | ILE 50: 3.012 GLU 121: 3.158 ASP 130: 3.269 PRO 181: 3.491 | ASP 29: 3.087 ILE 150: 3.024 GLY 48: 3.195 GLY 48: 3.166 GLY 48: 2.920 |
3NUJ | −8.6 | −8.1 | ASP 30: 3.004 LYS 45: 2.965 ARG 8: 3.222 ILE 50: 3.280 MET 46: 3.620 | ASP 29: 3.077 GLY 48: 3.091 ILE 50: 3.078 ASP 30: 2.861 GLY 48: 3.074 GLY 48: 3.084 ASP 25: 3.244 |
3NUO | −9.3 | −8.6 | ARG 8: 3.381 ARG 8: 2.944 | ASP 29: 2.965 ILE 50: 3.063 GLY 27: 3.018 GLY 48: 3.276 GLY 48: 2.780 GLY 48: 2.892 |
3PWM | −10.2 | −9.8 | ASP 30: 2.895 ILE 150: 3.098 ASP 30: 3.371 PRO 181: 3.317 | ASP 29: 2.930 GLY 48: 2.880 GLY 48: 3.237 ASP 29: 2.936 |
3S43 | −8.3 | −8.4 | ARG 8: 2.807 ASP 130: 2.982 LYS 145: 3.279 LYS 145: 3.094 ARG 187: 2.994 MET 146: 3.573 | ILE 50: 3.285 GLY 48: 3.113 GLY 48: 3.271 ASP 29: 2.817 GLY 48: 3.283 GLY 48: 2.794 |
3TH9 | −7.5 | −8.4 | ARG 8: 2.937 GLU 21: 3.160 GLY 48: 3.249 | ASP 29: 2.936 ASP 30: 3.356 ASP 29: 3.327 GLY 48: 3.200 |
3VF5 | −9.5 | −9.7 | ARG 8: 2.962 ARG 8: 3.185 GLY 48: 3.153 | ASP 29: 2.991 ASP 29: 3.370 GLY 27: 3.066 GLY 48: 2.894 ASP 25: 3.097 |
3VFB | −9.4 | −9.7 | ASP 29: 2.917 ASP 30: 3.371 LYS 45: 2.939 ASN 83: 3.022 ASP 30: 3.335 PRO 81: 3.522 | ARG 8: 2.792 ASP 30: 3.031 GLY 27: 3.015 GLY 27: 3.157 ASP 25: 2.967 GLY 48: 2.602 ASP 25: 2.962 ASP 25: 3.130 |
4GB2 | −7.5 | −8.3 | LYS 45: 3.352 LYS 45: 3.389 ARG 87: 3.383 ARG 87: 2.878 THR 91: 3.220 ASP 29: 3.216 | LYS 45: 3.121 GLY 48: 3.035 ARG 8: 3.365 ARG 8: 2.941 GLY 27: 3.034 GLY 48: 2.945 GLY 27: 3.289 |
4HDB | −11.4 | −11.2 | ASP 129: 3.175 ASN 130: 2.964 ASN 130: 3.386 LYS 145: 3.088 ASN 130: 3.073 | LYS 45: 3.400 GLY 48: 3.100 GLY 48: 3.110 GLY 48: 2.802 GLY 148: 3.261 |
4HDF | −10.8 | −11.2 | GLY 48: 3.356 GLY 48: 3.298 ARG 8: 3.335 ARG 8: 3.296 ASP 25: 3.295 GLU 21: 3.436 | GLY 27: 3.223 GLY 48: 3.146 GLY 27: 3.341 ASP 25: 3.124 GLY 48: 2.759 ASP 25: 3.462 GLY 48: 2.996 GLY 48: 2.989 ASP 30: 3.165 |
4HEG | −11.4 | −11.3 | GLY 48: 3.381 GLY 48: 3.243 ASP 30: 3.125 GLY 49: 3.551 | ASP 29: 2.882 GLY 48: 3.135 GLY 48: 3.037 GLY 48: 3.141 GLY 48: 3.166 GLY 48: 3.175 |
4YHQ | −13.8 | −12.2 | ARG 8: 3.193 ARG 8: 2.931 VAL 82: 3.170 ASP 29: 3.268 ASN 30: 3.325 ASN 30: 3.184 LYS 45: 3.258 LYS 45: 2.836 GLY 48: 3.261 GLY 48: 2.964 ASN 30: 3.208 ASN 30: 3.478 ASN 30: 3.384 | ASP 29: 2.803 GLY 48: 3.098 GLY 48: 2.935 GLY 48: 2.955 GLY 48: 3.178 GLY 48: 2.946 GLY 27: 2.629 GLY 48: 3.292 ASN 30: 2.953 |
