sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2012-05-17
| Name: | Geranyl diphosphate 2-C-methyltransferase |
|---|---|
| ID: | GPPMT_STRLS |
| AC: | D3KYU3 |
| Organism: | Streptomyces lasaliensis |
| Reign: | Bacteria |
| TaxID: | 324833 |
| EC Number: | 2.1.1.255 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| F | 100 % |
| B-Factor: | 52.966 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.111 | 364.500 |
| % Hydrophobic | % Polar |
|---|---|
| 62.96 | 37.04 |
| According to VolSite | |
| HET Code: | SFG |
|---|---|
| Formula: | C15H24N7O5 |
| Molecular weight: | 382.395 g/mol |
| DrugBank ID: | DB01910 |
| Buried Surface Area: | 79.19 % |
| Polar Surface area: | 214.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 28.3724 | -23.1306 | 21.6309 |
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 |
| C5' | CZ2 | TRP- 37 | 3.89 | 0 | Hydrophobic |
| C3' | CE2 | TRP- 37 | 3.47 | 0 | Hydrophobic |
| O | N | HIS- 57 | 3.36 | 163.55 | H-Bond (Protein Donor) |
| OXT | N | HIS- 57 | 3.47 | 143.22 | H-Bond (Protein Donor) |
| CB | CB | HIS- 57 | 3.24 | 0 | Hydrophobic |
| N | O | GLY- 113 | 3.46 | 143.4 | H-Bond (Ligand Donor) |
| O3' | NE2 | GLN- 140 | 3.44 | 133.49 | H-Bond (Protein Donor) |
| O2' | OE1 | GLN- 140 | 2.98 | 153.88 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASN- 163 | 2.58 | 163.79 | H-Bond (Ligand Donor) |
| C1' | CE | MET- 164 | 4.34 | 0 | Hydrophobic |
| N1 | N | MET- 164 | 2.92 | 173.93 | H-Bond (Protein Donor) |
| N | O | ASN- 180 | 2.83 | 134.27 | H-Bond (Ligand Donor) |
| NE | O | GLU- 181 | 3.16 | 147.78 | H-Bond (Ligand Donor) |
| C1' | CB | SER- 182 | 4.26 | 0 | Hydrophobic |
| C4' | CB | SER- 182 | 3.82 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 185 | 3.95 | 0 | Hydrophobic |
