sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2007-09-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.100 | 8.100 | 8.100 | 0.000 | 8.100 | 2 |
| 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: | 26.357 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.000 | 1073.250 |
| % Hydrophobic | % Polar |
|---|---|
| 43.08 | 56.92 |
| According to VolSite | |
| HET Code: | AAI |
|---|---|
| Formula: | C16H23N4O |
| Molecular weight: | 287.380 g/mol |
| DrugBank ID: | DB07330 |
| Buried Surface Area: | 63.75 % |
| Polar Surface area: | 76.21 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: | 4 |
| X | Y | Z |
|---|---|---|
| -24.547 | 64.55 | 26.3979 |
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 |
| C21 | CB | VAL- 101 | 4.04 | 0 | Hydrophobic |
| C21 | CG | GLU- 102 | 4 | 0 | Hydrophobic |
| N11 | O | GLY- 202 | 2.83 | 138.44 | H-Bond (Ligand Donor) |
| O12 | N | GLY- 202 | 2.91 | 164.03 | H-Bond (Protein Donor) |
| C18 | CD2 | TYR- 228 | 4.46 | 0 | Hydrophobic |
| C20 | CZ | TYR- 228 | 3.69 | 0 | Hydrophobic |
| C4 | CB | TYR- 235 | 3.55 | 0 | Hydrophobic |
| C7 | CB | ALA- 237 | 4.26 | 0 | Hydrophobic |
| C8 | CG | LYS- 242 | 4.16 | 0 | Hydrophobic |
| O12 | OG | SER- 243 | 2.99 | 147.76 | H-Bond (Protein Donor) |
| C14 | CE1 | TYR- 246 | 3.68 | 0 | Hydrophobic |
| C9 | CG | GLU- 327 | 3.83 | 0 | Hydrophobic |
