sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2009-01-04
| Name: | ATP-dependent dethiobiotin synthetase BioD |
|---|---|
| ID: | BIOD_MYCTU |
| AC: | P9WPQ5 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 27 % |
| B | 73 % |
| B-Factor: | 35.541 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.349 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.12 | 55.88 |
| According to VolSite | |
| HET Code: | DTB |
|---|---|
| Formula: | C10H17N2O3 |
| Molecular weight: | 213.254 g/mol |
| DrugBank ID: | DB03775 |
| Buried Surface Area: | 67.74 % |
| Polar Surface area: | 81.25 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -7.96107 | 20.8593 | -40.4637 |
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 |
| CE | CB | THR- 11 | 3.72 | 0 | Hydrophobic |
| CG | CG2 | THR- 11 | 4.25 | 0 | Hydrophobic |
| CA | CB | ALA- 73 | 3.75 | 0 | Hydrophobic |
| CG | CB | ALA- 73 | 4.32 | 0 | Hydrophobic |
| CT | CB | ALA- 110 | 3.55 | 0 | Hydrophobic |
| CD | CB | ALA- 110 | 4.35 | 0 | Hydrophobic |
| CB | CG2 | VAL- 115 | 4.21 | 0 | Hydrophobic |
| CA | CD2 | LEU- 143 | 3.91 | 0 | Hydrophobic |
| OI1 | N | GLY- 144 | 3.21 | 132.06 | H-Bond (Protein Donor) |
| OI1 | N | LEU- 146 | 2.91 | 167.89 | H-Bond (Protein Donor) |
| OI2 | N | ASN- 147 | 3.32 | 158.82 | H-Bond (Protein Donor) |
