sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 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 | 8 % |
| B | 92 % |
| B-Factor: | 21.826 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.771 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 39.16 | 60.84 |
| According to VolSite | |
| HET Code: | BD9 |
|---|---|
| Formula: | C40H55N9O5 |
| Molecular weight: | 741.922 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.46 % |
| Polar Surface area: | 198.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 24 |
| X | Y | Z |
|---|---|---|
| 5.79391 | 21.4835 | 23.4501 |
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 |
| C21 | CE2 | TYR- 44 | 4.01 | 0 | Hydrophobic |
| C40 | CB | SER- 48 | 3.82 | 0 | Hydrophobic |
| C11 | CE2 | TYR- 51 | 3.99 | 0 | Hydrophobic |
| C10 | CZ | TYR- 51 | 4.18 | 0 | Hydrophobic |
| O5 | NE1 | TRP- 52 | 2.89 | 159.7 | H-Bond (Protein Donor) |
| C22 | CB | ASP- 61 | 4.36 | 0 | Hydrophobic |
| C39 | CD2 | LEU- 96 | 4.16 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 96 | 4.16 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 99 | 4.23 | 0 | Hydrophobic |
| C4 | CG | ARG- 144 | 4.3 | 0 | Hydrophobic |
| C6 | CD | ARG- 144 | 3.88 | 0 | Hydrophobic |
| C2 | CE2 | PHE- 147 | 3.74 | 0 | Hydrophobic |
| C3 | SG | CYS- 148 | 3.95 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 195 | 4.22 | 0 | Hydrophobic |
| C2 | CE2 | TYR- 195 | 4.35 | 0 | Hydrophobic |
| C5 | SG | CYS- 196 | 3.93 | 0 | Hydrophobic |
| C27 | CE1 | TYR- 241 | 4.05 | 0 | Hydrophobic |
| C11 | CH2 | TRP- 244 | 3.91 | 0 | Hydrophobic |
| C7 | CZ3 | TRP- 244 | 3.82 | 0 | Hydrophobic |
| C5 | CH2 | TRP- 244 | 3.78 | 0 | Hydrophobic |
| C11 | CZ | PHE- 293 | 3.59 | 0 | Hydrophobic |
| C10 | CB | CYS- 314 | 3.85 | 0 | Hydrophobic |
| N8 | ZN | ZN- 332 | 2.28 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 332 | 3.41 | 87.38 | Pi/Cation |
| O5 | O | HOH- 463 | 2.67 | 134.5 | H-Bond (Ligand Donor) |
