sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2010-12-14
| 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 | 16 % |
| B | 84 % |
| B-Factor: | 33.474 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.987 | 1123.875 |
| % Hydrophobic | % Polar |
|---|---|
| 44.74 | 55.26 |
| According to VolSite | |
| HET Code: | 3PZ |
|---|---|
| Formula: | C29H29N5O3S |
| Molecular weight: | 527.637 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 33.3 % |
| Polar Surface area: | 99.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 4.94216 | 18.5314 | 27.4583 |
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 |
| N3 | ZN | ZN- 1 | 2.06 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 1 | 3.21 | 88.42 | Pi/Cation |
| O1 | OH | TYR- 44 | 3.15 | 148.32 | H-Bond (Protein Donor) |
| C3 | CD2 | LEU- 45 | 3.92 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 45 | 4.21 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 45 | 3.93 | 0 | Hydrophobic |
| C7 | CH2 | TRP- 52 | 3.93 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 107 | 4.41 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 289 | 3.74 | 0 | Hydrophobic |
| C9 | CZ | PHE- 289 | 3.97 | 0 | Hydrophobic |
| C21 | CE2 | PHE- 289 | 3.48 | 0 | Hydrophobic |
| C4 | CB | PHE- 289 | 3.5 | 0 | Hydrophobic |
| O2 | O | HOH- 378 | 3.35 | 149.98 | H-Bond (Protein Donor) |
