sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2004-01-22
| Name: | Geranylgeranyl transferase type-1 subunit beta |
|---|---|
| ID: | PGTB1_RAT |
| AC: | P53610 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 2.5.1.59 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| G | 4 % |
| H | 96 % |
| B-Factor: | 56.005 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.752 | 1636.875 |
| % Hydrophobic | % Polar |
|---|---|
| 41.86 | 58.14 |
| According to VolSite | |
| HET Code: | 778 |
|---|---|
| Formula: | C22H21ClN5O |
| Molecular weight: | 406.888 g/mol |
| DrugBank ID: | DB07227 |
| Buried Surface Area: | 55.26 % |
| Polar Surface area: | 66.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 70.0827 | 99.7494 | 29.7788 |
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 |
| CL31 | CB | ALA- 123 | 3.61 | 0 | Hydrophobic |
| O13 | NH1 | ARG- 173 | 2.92 | 147.99 | H-Bond (Protein Donor) |
| C20 | CD | ARG- 173 | 3.8 | 0 | Hydrophobic |
| C32 | CD | ARG- 173 | 4.37 | 0 | Hydrophobic |
| C27 | CG | ARG- 173 | 3.86 | 0 | Hydrophobic |
| C26 | CB | ARG- 173 | 3.69 | 0 | Hydrophobic |
| CL31 | CE2 | PHE- 174 | 3.79 | 0 | Hydrophobic |
| C30 | SG | CYS- 177 | 4.46 | 0 | Hydrophobic |
| CL31 | SG | CYS- 177 | 3.79 | 0 | Hydrophobic |
| N36 | NE2 | GLN- 212 | 3.35 | 140.67 | H-Bond (Protein Donor) |
| C27 | SG | CYS- 225 | 4.03 | 0 | Hydrophobic |
| N18 | ZN | ZN- 378 | 2.17 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 378 | 3.26 | 74.83 | Pi/Cation |
