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 | 7 % |
| B | 93 % |
| B-Factor: | 29.228 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.901 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.68 | 49.32 |
| According to VolSite | |
| HET Code: | BD6 |
|---|---|
| Formula: | C35H37N7O6 |
| Molecular weight: | 651.712 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.09 % |
| Polar Surface area: | 181.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 5.42292 | 21.5615 | 23.2829 |
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 |
| CAQ | CD2 | LEU- 45 | 4.15 | 0 | Hydrophobic |
| O | NE1 | TRP- 52 | 3.46 | 133.86 | H-Bond (Protein Donor) |
| OAF | NE1 | TRP- 52 | 3.17 | 141.77 | H-Bond (Protein Donor) |
| CAZ | CH2 | TRP- 52 | 3.67 | 0 | Hydrophobic |
| CZ2 | CD2 | LEU- 99 | 3.65 | 0 | Hydrophobic |
| CAI | CD | ARG- 144 | 4.03 | 0 | Hydrophobic |
| CAP | CD | ARG- 144 | 4.28 | 0 | Hydrophobic |
| CAG | CG | ARG- 144 | 3.31 | 0 | Hydrophobic |
| CAG | CG | GLN- 193 | 4.42 | 0 | Hydrophobic |
| CAJ | SG | CYS- 196 | 3.47 | 0 | Hydrophobic |
| CAX | CZ3 | TRP- 244 | 3.5 | 0 | Hydrophobic |
| CAZ | CE2 | PHE- 289 | 3.95 | 0 | Hydrophobic |
| CAR | CB | PHE- 289 | 4.46 | 0 | Hydrophobic |
| NBF | ZN | ZN- 332 | 2.07 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 332 | 3.17 | 81.84 | Pi/Cation |
| OAF | O | HOH- 353 | 2.97 | 155.48 | H-Bond (Ligand Donor) |
