sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.720 Å
X-ray
2012-10-10
| Name: | Poly [ADP-ribose] polymerase 1 |
|---|---|
| ID: | PARP1_HUMAN |
| AC: | P09874 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.4.2.30 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 18.907 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.195 | 1134.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.30 | 49.70 |
| According to VolSite | |
| HET Code: | 15S |
|---|---|
| Formula: | C27H30FN4O3 |
| Molecular weight: | 477.550 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.99 % |
| Polar Surface area: | 82.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -36.7504 | 50.9443 | -70.3338 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| CAF | CB | ASP- 105 | 3.48 | 0 | Hydrophobic |
| CAM | CB | ASP- 105 | 4.25 | 0 | Hydrophobic |
| FAE | CD1 | LEU- 108 | 3.43 | 0 | Hydrophobic |
| OAC | N | GLY- 202 | 2.77 | 168.88 | H-Bond (Protein Donor) |
| NAU | O | GLY- 202 | 2.56 | 120.65 | H-Bond (Ligand Donor) |
| CAL | CB | ARG- 217 | 3.96 | 0 | Hydrophobic |
| CBB | CB | ALA- 219 | 3.94 | 0 | Hydrophobic |
| CAM | CB | ALA- 219 | 3.87 | 0 | Hydrophobic |
| FAE | CG | PRO- 220 | 3.42 | 0 | Hydrophobic |
| CB | CE1 | TYR- 228 | 3.28 | 0 | Hydrophobic |
| CAP | CD2 | TYR- 235 | 3.87 | 0 | Hydrophobic |
| CB | CE1 | TYR- 235 | 4.39 | 0 | Hydrophobic |
| CBC | CB | TYR- 235 | 3.7 | 0 | Hydrophobic |
| CAI | CB | ALA- 237 | 3.92 | 0 | Hydrophobic |
| CAG | CD | LYS- 242 | 3.63 | 0 | Hydrophobic |
| OAC | OG | SER- 243 | 2.54 | 167.86 | H-Bond (Protein Donor) |
| CAP | CZ | TYR- 246 | 3.72 | 0 | Hydrophobic |
| CAH | CG | GLU- 327 | 4.12 | 0 | Hydrophobic |
