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
2008-02-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.160 | 6.160 | 6.160 | 0.000 | 6.160 | 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: | 24.472 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.035 | 664.875 |
| % Hydrophobic | % Polar |
|---|---|
| 44.16 | 55.84 |
| According to VolSite | |
| HET Code: | P34 |
|---|---|
| Formula: | C17H18N3O2 |
| Molecular weight: | 296.344 g/mol |
| DrugBank ID: | DB08348 |
| Buried Surface Area: | 50.55 % |
| Polar Surface area: | 62.64 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: | 3 |
| X | Y | Z |
|---|---|---|
| 19.3773 | -6.81709 | 13.2457 |
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- 385 | 2.86 | 162.83 | H-Bond (Protein Donor) |
| NAN | O | GLY- 385 | 2.72 | 128.69 | H-Bond (Ligand Donor) |
| CAU | CB | TYR- 414 | 4.13 | 0 | Hydrophobic |
| CAF | CB | TYR- 414 | 3.92 | 0 | Hydrophobic |
| CAT | CB | TYR- 414 | 3.5 | 0 | Hydrophobic |
| CAH | CB | ALA- 416 | 3.88 | 0 | Hydrophobic |
| CAE | CG | LYS- 421 | 4.01 | 0 | Hydrophobic |
| OAD | OG | SER- 422 | 2.59 | 144.49 | H-Bond (Protein Donor) |
| CAJ | CB | TYR- 425 | 4.1 | 0 | Hydrophobic |
| CAI | CZ | TYR- 425 | 3.44 | 0 | Hydrophobic |
| CAR | CB | TYR- 425 | 3.88 | 0 | Hydrophobic |
| CAE | CG | GLU- 514 | 3.61 | 0 | Hydrophobic |
