sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 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: | 28.738 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.088 | 516.375 |
| % Hydrophobic | % Polar |
|---|---|
| 52.94 | 47.06 |
| According to VolSite | |
| HET Code: | BD7 |
|---|---|
| Formula: | C33H36N6O7 |
| Molecular weight: | 628.675 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.02 % |
| Polar Surface area: | 185.97 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: | 15 |
| X | Y | Z |
|---|---|---|
| 5.67291 | 21.0987 | 23.4183 |
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 |
| CBA | CD2 | LEU- 45 | 4.11 | 0 | Hydrophobic |
| CAP | CD2 | LEU- 45 | 4.28 | 0 | Hydrophobic |
| OAF | NE1 | TRP- 52 | 3.02 | 155.71 | H-Bond (Protein Donor) |
| CBA | CH2 | TRP- 52 | 3.76 | 0 | Hydrophobic |
| CE2 | CD2 | LEU- 96 | 3.35 | 0 | Hydrophobic |
| OH | O | ARG- 144 | 2.79 | 129.41 | H-Bond (Ligand Donor) |
| CAK | CG | ARG- 144 | 3.63 | 0 | Hydrophobic |
| CE2 | CG | ARG- 144 | 3.7 | 0 | Hydrophobic |
| CD2 | CD | ARG- 144 | 3.67 | 0 | Hydrophobic |
| CAH | CD | ARG- 144 | 3.57 | 0 | Hydrophobic |
| CE2 | SG | CYS- 148 | 3.81 | 0 | Hydrophobic |
| CAK | SG | CYS- 196 | 3.45 | 0 | Hydrophobic |
| CZ | SG | CYS- 196 | 3.49 | 0 | Hydrophobic |
| CB | CZ2 | TRP- 244 | 4.41 | 0 | Hydrophobic |
| CAX | CE2 | TRP- 244 | 3.41 | 0 | Hydrophobic |
| CBM | CH2 | TRP- 244 | 3.15 | 0 | Hydrophobic |
| CBA | CE2 | PHE- 289 | 4.15 | 0 | Hydrophobic |
| NBF | ZN | ZN- 332 | 2.06 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 332 | 3.18 | 86.51 | Pi/Cation |
| OAF | O | HOH- 380 | 3.08 | 163.68 | H-Bond (Ligand Donor) |
