sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2015-09-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.620 | 9.620 | 9.620 | 0.000 | 9.620 | 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: | 44.775 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.706 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.76 | 58.24 |
| According to VolSite | |
| HET Code: | 09L |
|---|---|
| Formula: | C24H23FN4O3 |
| Molecular weight: | 434.463 g/mol |
| DrugBank ID: | DB09074 |
| Buried Surface Area: | 61.52 % |
| Polar Surface area: | 82.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -2.54125 | 39.6621 | 14.1079 |
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 |
| OAD | N | GLY- 863 | 2.92 | 153.38 | H-Bond (Protein Donor) |
| NAH | O | GLY- 863 | 2.81 | 165.78 | H-Bond (Ligand Donor) |
| OAB | N | ARG- 878 | 2.89 | 155.05 | H-Bond (Protein Donor) |
| CAJ | CB | ARG- 878 | 4.18 | 0 | Hydrophobic |
| FAA | CE2 | TYR- 889 | 3.36 | 0 | Hydrophobic |
| OAC | N | TYR- 896 | 2.83 | 169.81 | H-Bond (Protein Donor) |
| FAA | CE1 | TYR- 896 | 3.34 | 0 | Hydrophobic |
| CAU | CD1 | TYR- 896 | 3.24 | 0 | Hydrophobic |
| CAS | CB | TYR- 896 | 3.94 | 0 | Hydrophobic |
| CBB | CB | TYR- 896 | 3.65 | 0 | Hydrophobic |
| CBD | CB | ALA- 898 | 4.05 | 0 | Hydrophobic |
| CBF | CG | LYS- 903 | 4.22 | 0 | Hydrophobic |
| OAD | OG | SER- 904 | 2.77 | 170.94 | H-Bond (Protein Donor) |
| CAV | CE1 | TYR- 907 | 3.35 | 0 | Hydrophobic |
| CAZ | CE2 | TYR- 907 | 3.46 | 0 | Hydrophobic |
| CBE | CG | GLU- 988 | 4.06 | 0 | Hydrophobic |
