sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2002-11-01
| 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 | 18 % |
| H | 82 % |
| B-Factor: | 65.572 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.889 | 1201.500 |
| % Hydrophobic | % Polar |
|---|---|
| 40.17 | 59.83 |
| According to VolSite | |
| HET Code: | CYS_VAL_ILE_LEU_GER |
|---|---|
| Formula: | C20H38N4O5S |
| Molecular weight: | 446.605 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 36.64 % |
| Polar Surface area: | 193.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 5 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 74.838 | 106.816 | 30.1303 |
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 |
| CB | CD2 | LEU- 43 | 3.98 | 0 | Hydrophobic |
| CD1 | CB | SER- 46 | 4.42 | 0 | Hydrophobic |
| CD1 | CG2 | THR- 49 | 4.23 | 0 | Hydrophobic |
| CD1 | CZ | PHE- 53 | 4.33 | 0 | Hydrophobic |
| CD1 | CB | ALA- 123 | 4.3 | 0 | Hydrophobic |
| CD2 | CB | ALA- 123 | 4.3 | 0 | Hydrophobic |
| CD1 | CE | MET- 124 | 3.93 | 0 | Hydrophobic |
| O | NE2 | GLN- 167 | 3.25 | 175.68 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 173 | 2.83 | 136.76 | H-Bond (Protein Donor) |
| CD2 | CE2 | PHE- 174 | 4.18 | 0 | Hydrophobic |
| CG2 | CD1 | LEU- 320 | 4.28 | 0 | Hydrophobic |
| CG2 | CD1 | LEU- 320 | 4.04 | 0 | Hydrophobic |
| CD1 | CD1 | LEU- 320 | 3.47 | 0 | Hydrophobic |
