sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2013-06-12
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.520 | 8.520 | 8.520 | 0.000 | 8.520 | 1 |
| 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: | 26.034 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.390 | 691.875 |
| % Hydrophobic | % Polar |
|---|---|
| 41.46 | 58.54 |
| According to VolSite | |
| HET Code: | 1WQ |
|---|---|
| Formula: | C21H22ClN2O2 |
| Molecular weight: | 369.865 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.31 % |
| Polar Surface area: | 42.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 14.9402 | -4.67685 | -7.8415 |
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 |
| C16 | CB | ASP- 766 | 3.88 | 0 | Hydrophobic |
| C21 | CB | LEU- 769 | 3.89 | 0 | Hydrophobic |
| CL | CD1 | LEU- 769 | 3.58 | 0 | Hydrophobic |
| N25 | O | GLY- 863 | 2.77 | 172.52 | H-Bond (Ligand Donor) |
| O27 | N | GLY- 863 | 3.03 | 162.02 | H-Bond (Protein Donor) |
| CL | CB | ARG- 878 | 3.68 | 0 | Hydrophobic |
| C19 | CB | ARG- 878 | 3.85 | 0 | Hydrophobic |
| C2 | CB | TYR- 896 | 3.77 | 0 | Hydrophobic |
| C5 | CB | TYR- 896 | 4.16 | 0 | Hydrophobic |
| C1 | CB | ALA- 898 | 4.15 | 0 | Hydrophobic |
| O27 | OG | SER- 904 | 2.81 | 155.15 | H-Bond (Protein Donor) |
| C23 | CB | TYR- 907 | 4.14 | 0 | Hydrophobic |
| C2 | CE2 | TYR- 907 | 4.43 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 907 | 3.95 | 0 | Aromatic Face/Face |
