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
2008-01-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.160 | 7.160 | 7.160 | 0.000 | 7.160 | 1 |
| Name: | Poly [ADP-ribose] polymerase 3 |
|---|---|
| ID: | PARP3_HUMAN |
| AC: | Q9Y6F1 |
| 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: | 21.307 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.924 | 722.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.79 | 54.21 |
| According to VolSite | |
| HET Code: | KU8 |
|---|---|
| Formula: | C21H22FN4O2 |
| Molecular weight: | 381.423 g/mol |
| DrugBank ID: | DB08058 |
| Buried Surface Area: | 62.29 % |
| Polar Surface area: | 78.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| 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 |
|---|---|---|
| 20.2918 | -5.93754 | 10.5748 |
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 |
| O1B | N | GLY- 385 | 2.65 | 137.98 | H-Bond (Protein Donor) |
| N1S | O | GLY- 385 | 2.91 | 162.01 | H-Bond (Ligand Donor) |
| F1C | CB | SER- 405 | 3.81 | 0 | Hydrophobic |
| O1A | N | TYR- 414 | 2.92 | 159.68 | H-Bond (Protein Donor) |
| F1C | CE2 | TYR- 414 | 3.73 | 0 | Hydrophobic |
| C1W | CD2 | TYR- 414 | 3.2 | 0 | Hydrophobic |
| C1J | CB | TYR- 414 | 3.69 | 0 | Hydrophobic |
| C1H | CB | TYR- 414 | 3.65 | 0 | Hydrophobic |
| C1I | CB | ALA- 416 | 4.02 | 0 | Hydrophobic |
| C1E | CG | LYS- 421 | 3.93 | 0 | Hydrophobic |
| O1B | OG | SER- 422 | 2.96 | 164.66 | H-Bond (Protein Donor) |
| C1P | CE1 | TYR- 425 | 3.48 | 0 | Hydrophobic |
| C1D | CG | GLU- 514 | 3.52 | 0 | Hydrophobic |
