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 | 6 % |
| B | 94 % |
| B-Factor: | 25.457 |
|---|---|
| Number of residues: | 49 |
| Including | |
| Standard Amino Acids: | 47 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.119 | 580.500 |
| % Hydrophobic | % Polar |
|---|---|
| 55.81 | 44.19 |
| According to VolSite | |
| HET Code: | BD8 |
|---|---|
| Formula: | C43H57N7O5 |
| Molecular weight: | 751.957 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.56 % |
| Polar Surface area: | 169.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 24 |
| X | Y | Z |
|---|---|---|
| 5.08105 | 22.1855 | 23.8513 |
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 |
| CAA | CE2 | TYR- 30 | 3.48 | 0 | Hydrophobic |
| CAX | CD1 | LEU- 45 | 4.14 | 0 | Hydrophobic |
| CBC | CD2 | LEU- 45 | 4.13 | 0 | Hydrophobic |
| CAR | CB | SER- 48 | 4.2 | 0 | Hydrophobic |
| CAW | CE3 | TRP- 52 | 3.76 | 0 | Hydrophobic |
| CBC | CZ3 | TRP- 52 | 3.86 | 0 | Hydrophobic |
| CAY | CZ3 | TRP- 52 | 3.79 | 0 | Hydrophobic |
| CAT | CD2 | LEU- 96 | 4 | 0 | Hydrophobic |
| CAR | CD1 | LEU- 96 | 4.03 | 0 | Hydrophobic |
| OAG | OH | TYR- 97 | 2.81 | 149.31 | H-Bond (Ligand Donor) |
| CBF | CD2 | LEU- 99 | 4.33 | 0 | Hydrophobic |
| CZ | CG | ARG- 144 | 3.48 | 0 | Hydrophobic |
| CE2 | CD | ARG- 144 | 3.44 | 0 | Hydrophobic |
| CBF | CE2 | PHE- 147 | 4.35 | 0 | Hydrophobic |
| CZ | SG | CYS- 196 | 3.81 | 0 | Hydrophobic |
| CBI | CH2 | TRP- 244 | 4.31 | 0 | Hydrophobic |
| CAZ | CB | ASP- 287 | 4.25 | 0 | Hydrophobic |
| CAW | CG | PRO- 288 | 3.77 | 0 | Hydrophobic |
| CAY | CB | PHE- 289 | 4.32 | 0 | Hydrophobic |
| CBE | CE2 | PHE- 289 | 3.83 | 0 | Hydrophobic |
| CBI | CE2 | PHE- 289 | 4.3 | 0 | Hydrophobic |
| CBC | CB | PHE- 289 | 3.82 | 0 | Hydrophobic |
| CAI | CB | CYS- 314 | 3.3 | 0 | Hydrophobic |
| DuAr | ZN | ZN- 332 | 2.78 | 85.41 | Pi/Cation |
