sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2009-06-20
| Name: | Geranylgeranyl transferase type-2 subunit beta |
|---|---|
| ID: | PGTB2_RAT |
| AC: | Q08603 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 2.5.1.60 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 14 % |
| B | 86 % |
| B-Factor: | 32.135 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.977 | 948.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.04 | 51.96 |
| According to VolSite | |
| HET Code: | BD5 |
|---|---|
| Formula: | C35H34N3O8 |
| Molecular weight: | 624.660 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 47.76 % |
| Polar Surface area: | 177.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 6.50587 | 20.8104 | 23.2882 |
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 |
| C17 | CB | SER- 48 | 3.86 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 96 | 3.8 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 96 | 3.98 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 99 | 3.78 | 0 | Hydrophobic |
| C28 | CD | ARG- 144 | 4.33 | 0 | Hydrophobic |
| C7 | CD | ARG- 144 | 3.86 | 0 | Hydrophobic |
| C31 | CD | ARG- 144 | 3.88 | 0 | Hydrophobic |
| C30 | CG | ARG- 144 | 3.42 | 0 | Hydrophobic |
| O11 | NH1 | ARG- 144 | 3.28 | 141.46 | H-Bond (Protein Donor) |
| C4 | SG | CYS- 148 | 4.04 | 0 | Hydrophobic |
| C30 | CG | GLN- 193 | 4.08 | 0 | Hydrophobic |
| C29 | SG | CYS- 196 | 3.87 | 0 | Hydrophobic |
| C2 | SG | CYS- 196 | 4.49 | 0 | Hydrophobic |
| C25 | CH2 | TRP- 244 | 4.4 | 0 | Hydrophobic |
| C27 | CH2 | TRP- 244 | 2.88 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 289 | 4.23 | 0 | Hydrophobic |
