Research Article
In Silico Investigation of Potential PARP-1 Inhibitors from Traditional Chinese Medicine
Table 2
H-bond occupancy for key residues of PARP-1 protein with top three candidates and A927929 overall 40 ns molecular dynamics simulation.
| | Name | H-bond interaction | Occupancy |
| | A927929 | His201:ND1 | /H44 | 58% | | Gly202:HN | /N24 | 88% | | Gly202:HN | /O25 | 100% | | Gly202:O | /H44 | 86% | | Ser243:HG1 | /O25 | 100% |
| | Isopraeroside IV | Asp105:OD1 | /H53 | 32% | | Asp105:OD2 | /H53 | 5% | | His201:HE2 | /O27 | 17% | | Gly202:HN | /O15 | 87% | | Gly202:O | /H51 | 44% | | Ser243:HG1 | /O15 | 63% | | His248:HE2 | /O28 | 71% | | His248:HE2 | /O29 | 22% |
| | Picrasidine M | Tyr228:HH | /N27 | 66% | | Tyr228:HH | /O34 | 87% | | Lys242:HZ3 | /O17 | 20% | | Tyr246:HH | /N26 | 11% |
| | Aurantiamide acetate | Gly202:HN | /O32 | 6% | | Gly202:HN | /O34 | 78% | | Tyr228:HH | /O8 | 35% | | Ser243:HG1 | /O34 | 55% |
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H-bond occupancy cutoff: 0.3 nm.
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