sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.850 Å
X-ray
2013-07-04
| Name: | PAB-dependent poly(A)-specific ribonuclease subunit pan3 |
|---|---|
| ID: | PAN3_NEUCR |
| AC: | Q7SDP4 |
| Organism: | Neurospora crassa |
| Reign: | Eukaryota |
| TaxID: | 367110 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 77.181 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.915 | 783.000 |
| % Hydrophobic | % Polar |
|---|---|
| 48.71 | 51.29 |
| According to VolSite | |
| HET Code: | AGS |
|---|---|
| Formula: | C10H14N5O12P3S |
| Molecular weight: | 521.231 g/mol |
| DrugBank ID: | DB02930 |
| Buried Surface Area: | 66.16 % |
| Polar Surface area: | 329.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -49.6153 | 23.5432 | 30.7875 |
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 |
| C4' | CB | LEU- 270 | 4.1 | 0 | Hydrophobic |
| C1' | CB | LEU- 270 | 4.37 | 0 | Hydrophobic |
| C5' | CB | MET- 287 | 3.89 | 0 | Hydrophobic |
| C4' | CG | MET- 287 | 4.34 | 0 | Hydrophobic |
| C1' | CG | MET- 287 | 4.32 | 0 | Hydrophobic |
| O1A | NH2 | ARG- 302 | 3.24 | 128.33 | H-Bond (Protein Donor) |
| O1A | NH1 | ARG- 302 | 2.59 | 165.64 | H-Bond (Protein Donor) |
| O2A | NH1 | ARG- 302 | 3.3 | 138.72 | H-Bond (Protein Donor) |
| O1A | CZ | ARG- 302 | 3.33 | 0 | Ionic (Protein Cationic) |
| N6 | O | ASP- 352 | 3.23 | 160.57 | H-Bond (Ligand Donor) |
| N1 | N | HIS- 354 | 3.21 | 169.46 | H-Bond (Protein Donor) |
| C3' | CG2 | THR- 359 | 3.71 | 0 | Hydrophobic |
| O3G | NZ | LYS- 413 | 3.24 | 128.95 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 413 | 3.04 | 158.91 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 413 | 3.24 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 413 | 3.61 | 0 | Ionic (Protein Cationic) |
| C2' | CG2 | ILE- 415 | 4.32 | 0 | Hydrophobic |
| O2G | MG | MG- 1648 | 2.22 | 0 | Metal Acceptor |
| O2A | MG | MG- 1648 | 2.29 | 0 | Metal Acceptor |
