sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2012-08-29
| 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 | 9 % |
| B | 91 % |
| B-Factor: | 26.954 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.010 | 982.125 |
| % Hydrophobic | % Polar |
|---|---|
| 47.42 | 52.58 |
| According to VolSite | |
| HET Code: | 7TR |
|---|---|
| Formula: | C34H38N6O5S |
| Molecular weight: | 642.768 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 42.69 % |
| Polar Surface area: | 129.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 0 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 4.66198 | 20.4087 | 26.5896 |
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 |
| OAH | OH | TYR- 44 | 3.19 | 144.61 | H-Bond (Protein Donor) |
| CAV | CD2 | LEU- 45 | 4.12 | 0 | Hydrophobic |
| CAQ | CD2 | LEU- 45 | 3.83 | 0 | Hydrophobic |
| CAZ | CH2 | TRP- 52 | 4.21 | 0 | Hydrophobic |
| CAB | CD2 | LEU- 99 | 4.24 | 0 | Hydrophobic |
| CAB | CD2 | PHE- 147 | 3.82 | 0 | Hydrophobic |
| CAB | SG | CYS- 148 | 4.1 | 0 | Hydrophobic |
| CAA | CD2 | TYR- 195 | 4.04 | 0 | Hydrophobic |
| CAA | SG | CYS- 196 | 3.6 | 0 | Hydrophobic |
| CAB | SG | CYS- 196 | 4.4 | 0 | Hydrophobic |
| CAA | CZ2 | TRP- 244 | 3.47 | 0 | Hydrophobic |
| CBB | CZ | PHE- 289 | 4.25 | 0 | Hydrophobic |
| CAZ | CE2 | PHE- 289 | 4.01 | 0 | Hydrophobic |
| CBG | CB | PHE- 289 | 3.45 | 0 | Hydrophobic |
| NBC | ZN | ZN- 401 | 2.05 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 401 | 3.17 | 83.19 | Pi/Cation |
