sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2014-01-28
| Name: | Diterpene synthase |
|---|---|
| ID: | TUBOL_MYCTU |
| AC: | P9WJ61 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 3.1.7.8 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 55.261 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.618 | 691.875 |
| % Hydrophobic | % Polar |
|---|---|
| 44.39 | 55.61 |
| According to VolSite | |
| HET Code: | B29 |
|---|---|
| Formula: | C20H14O8P2 |
| Molecular weight: | 444.268 g/mol |
| DrugBank ID: | DB07410 |
| Buried Surface Area: | 62.05 % |
| Polar Surface area: | 179.37 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -17.5282 | -18.5699 | 21.8243 |
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 |
| CAH | CB | PHE- 33 | 3.98 | 0 | Hydrophobic |
| OAF | OG1 | THR- 36 | 2.62 | 151.67 | H-Bond (Protein Donor) |
| CAQ | CB | GLN- 52 | 4.17 | 0 | Hydrophobic |
| CAK | CG | GLN- 52 | 3.42 | 0 | Hydrophobic |
| CAY | CB | ALA- 55 | 4.13 | 0 | Hydrophobic |
| CAI | CB | SER- 59 | 3.81 | 0 | Hydrophobic |
| CAH | CG2 | ILE- 78 | 4.32 | 0 | Hydrophobic |
| CAS | CD1 | PHE- 79 | 3.9 | 0 | Hydrophobic |
| CAR | CE1 | PHE- 79 | 3.21 | 0 | Hydrophobic |
| CAL | CZ | TYR- 90 | 3.46 | 0 | Hydrophobic |
| CAM | CB | GLN- 93 | 4.16 | 0 | Hydrophobic |
| CAJ | CB | ALA- 94 | 4.44 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 100 | 4.41 | 0 | Hydrophobic |
| CAI | CD2 | LEU- 101 | 4.3 | 0 | Hydrophobic |
| OAD | MG | MG- 403 | 2.31 | 0 | Metal Acceptor |
| OAB | MG | MG- 403 | 2.45 | 0 | Metal Acceptor |
