sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.420 Å
X-ray
2009-07-31
| Name: | Dihydrolipoyl dehydrogenase |
|---|---|
| ID: | DLDH_MYCTU |
| AC: | P9WHH9 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 1.8.1.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 95 % |
| B | 5 % |
| B-Factor: | 24.928 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.360 | 1221.750 |
| % Hydrophobic | % Polar |
|---|---|
| 42.82 | 57.18 |
| According to VolSite | |
| HET Code: | 3II |
|---|---|
| Formula: | C32H34Cl2N4O5 |
| Molecular weight: | 625.542 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.51 % |
| Polar Surface area: | 91.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -28.0949 | -2.04858 | 33.2168 |
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 |
| CL40 | CD | ARG- 147 | 3.8 | 0 | Hydrophobic |
| C18 | CB | ALA- 181 | 4.28 | 0 | Hydrophobic |
| C4 | CB | ALA- 181 | 3.38 | 0 | Hydrophobic |
| C1 | CG1 | ILE- 182 | 3.59 | 0 | Hydrophobic |
| C28 | CB | ASN- 209 | 3.54 | 0 | Hydrophobic |
| CL40 | CB | ALA- 270 | 3.89 | 0 | Hydrophobic |
| CL43 | CG | PRO- 271 | 4.26 | 0 | Hydrophobic |
| CL43 | CB | ARG- 288 | 3.8 | 0 | Hydrophobic |
| C41 | CB | ARG- 288 | 3.96 | 0 | Hydrophobic |
| CL43 | CB | ALA- 290 | 3.49 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 314 | 4.33 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 314 | 3.39 | 0 | Hydrophobic |
| O22 | N | GLN- 315 | 3.04 | 156.51 | H-Bond (Protein Donor) |
| C9 | CG | LEU- 316 | 4.06 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 316 | 3.5 | 0 | Hydrophobic |
| C18 | CB | ARG- 347 | 3.64 | 0 | Hydrophobic |
| C30 | CD | ARG- 347 | 3.71 | 0 | Hydrophobic |
| C6 | CD1 | PHE- 350 | 3.68 | 0 | Hydrophobic |
| C19 | C1' | FAD- 480 | 4.49 | 0 | Hydrophobic |
