sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2008-02-06
| 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 | 13 % |
| B | 87 % |
| B-Factor: | 34.495 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.149 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 54.61 | 45.39 |
| According to VolSite | |
| HET Code: | CX1 |
|---|---|
| Formula: | C33H34N5O7 |
| Molecular weight: | 612.652 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.61 % |
| Polar Surface area: | 176.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 6.39356 | 20.5564 | 23.4729 |
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 |
| C7 | CD2 | LEU- 96 | 4.22 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 96 | 4.06 | 0 | Hydrophobic |
| N30 | OH | TYR- 97 | 3.04 | 152.57 | H-Bond (Ligand Donor) |
| C1 | CD2 | LEU- 99 | 3.89 | 0 | Hydrophobic |
| C34 | CD | ARG- 144 | 3.97 | 0 | Hydrophobic |
| C37 | CD | ARG- 144 | 4.35 | 0 | Hydrophobic |
| C7 | CD | ARG- 144 | 3.62 | 0 | Hydrophobic |
| C35 | CG | ARG- 144 | 3.42 | 0 | Hydrophobic |
| O11 | NH1 | ARG- 144 | 3.09 | 152.57 | H-Bond (Protein Donor) |
| C6 | SG | CYS- 148 | 4.47 | 0 | Hydrophobic |
| C35 | CG | GLN- 193 | 4.44 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 195 | 3.23 | 0 | Hydrophobic |
| C36 | SG | CYS- 196 | 3.81 | 0 | Hydrophobic |
| C5 | SG | CYS- 196 | 4.11 | 0 | Hydrophobic |
| C4 | SG | CYS- 196 | 3.62 | 0 | Hydrophobic |
| O27 | OH | TYR- 241 | 3.43 | 142.12 | H-Bond (Protein Donor) |
| C38 | CH2 | TRP- 244 | 3.26 | 0 | Hydrophobic |
