sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2007-09-21
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.300 | 8.460 | 8.300 | 0.220 | 8.770 | 3 |
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 30.366 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.735 | 938.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.45 | 57.55 |
| According to VolSite | |
| HET Code: | 78P |
|---|---|
| Formula: | C13H17N4O |
| Molecular weight: | 245.300 g/mol |
| DrugBank ID: | DB07232 |
| Buried Surface Area: | 62.36 % |
| Polar Surface area: | 88.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 25.8112 | 65.1272 | 8.85694 |
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 |
| N11 | O | GLY- 202 | 3.12 | 159.5 | H-Bond (Ligand Donor) |
| O12 | N | GLY- 202 | 2.71 | 157.46 | H-Bond (Protein Donor) |
| C16 | CD2 | TYR- 228 | 3.77 | 0 | Hydrophobic |
| C17 | CD2 | TYR- 235 | 3.94 | 0 | Hydrophobic |
| C16 | CD1 | TYR- 235 | 3.76 | 0 | Hydrophobic |
| C3 | CB | TYR- 235 | 3.59 | 0 | Hydrophobic |
| C1 | CB | ALA- 237 | 3.89 | 0 | Hydrophobic |
| C1 | CG | LYS- 242 | 3.73 | 0 | Hydrophobic |
| O12 | OG | SER- 243 | 3.01 | 159.38 | H-Bond (Protein Donor) |
| C18 | CE1 | TYR- 246 | 3.77 | 0 | Hydrophobic |
| C2 | CG | GLU- 327 | 3.72 | 0 | Hydrophobic |
