sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2009-12-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.480 | 7.480 | 7.480 | 0.000 | 7.480 | 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: | 40.446 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.125 | 995.625 |
| % Hydrophobic | % Polar |
|---|---|
| 47.80 | 52.20 |
| According to VolSite | |
| HET Code: | L3L |
|---|---|
| Formula: | C14H18N3O2 |
| Molecular weight: | 260.312 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.97 % |
| Polar Surface area: | 80.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -25.2416 | 64.6826 | 25.9255 |
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 |
| N17 | O | GLY- 202 | 3.03 | 146.9 | H-Bond (Ligand Donor) |
| O19 | N | GLY- 202 | 2.97 | 158.29 | H-Bond (Protein Donor) |
| N15 | O | GLY- 227 | 3.34 | 133.3 | H-Bond (Ligand Donor) |
| C10 | CD1 | TYR- 235 | 4.11 | 0 | Hydrophobic |
| C3 | CB | TYR- 235 | 3.75 | 0 | Hydrophobic |
| C4 | CB | TYR- 235 | 3.46 | 0 | Hydrophobic |
| C1 | CB | ALA- 237 | 4.36 | 0 | Hydrophobic |
| C1 | CG | LYS- 242 | 3.85 | 0 | Hydrophobic |
| O19 | OG | SER- 243 | 2.91 | 171.32 | H-Bond (Protein Donor) |
| C11 | CE1 | TYR- 246 | 4.16 | 0 | Hydrophobic |
| C5 | CE2 | TYR- 246 | 3.32 | 0 | Hydrophobic |
| C3 | CG | GLU- 327 | 3.62 | 0 | Hydrophobic |
