sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 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 | 10 % |
| B | 90 % |
| B-Factor: | 39.427 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.899 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 54.30 | 45.70 |
| According to VolSite | |
| HET Code: | 7TQ |
|---|---|
| Formula: | C37H36N6O5S |
| Molecular weight: | 676.784 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 38.86 % |
| Polar Surface area: | 138.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 1 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 4.50576 | 21.6023 | 25.7237 |
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 |
| OAF | OH | TYR- 44 | 2.73 | 161.54 | H-Bond (Protein Donor) |
| CAU | CD2 | LEU- 45 | 4.32 | 0 | Hydrophobic |
| CBB | CD2 | LEU- 45 | 3.8 | 0 | Hydrophobic |
| CBB | CH2 | TRP- 52 | 4.42 | 0 | Hydrophobic |
| CAL | CD2 | LEU- 99 | 3.74 | 0 | Hydrophobic |
| CAK | CE2 | PHE- 147 | 3.07 | 0 | Hydrophobic |
| CAI | CE2 | TYR- 195 | 3.41 | 0 | Hydrophobic |
| CBA | CZ | PHE- 289 | 3.65 | 0 | Hydrophobic |
| CBJ | CB | PHE- 289 | 3.71 | 0 | Hydrophobic |
| CAO | CE2 | PHE- 289 | 3.37 | 0 | Hydrophobic |
| CAH | CB | CYS- 314 | 4.2 | 0 | Hydrophobic |
| NBE | ZN | ZN- 401 | 2.27 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 401 | 3.34 | 74.52 | Pi/Cation |
