sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.130 Å
X-ray
2009-08-31
| Name: | Pantothenate synthetase |
|---|---|
| ID: | PANC_MYCTU |
| AC: | P9WIL5 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 6.3.2.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 30.725 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.910 | 604.125 |
| % Hydrophobic | % Polar |
|---|---|
| 48.04 | 51.96 |
| According to VolSite | |
| HET Code: | FG4 |
|---|---|
| Formula: | C21H16NO6 |
| Molecular weight: | 378.355 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.8 % |
| Polar Surface area: | 93.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 0.938714 | -10.5906 | 36.2995 |
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 | PRO- 38 | 4.17 | 0 | Hydrophobic |
| CAN | CB | THR- 39 | 4.48 | 0 | Hydrophobic |
| CAN | CB | MET- 40 | 4.4 | 0 | Hydrophobic |
| CAX | CG | MET- 40 | 3.85 | 0 | Hydrophobic |
| O | NE2 | HIS- 44 | 2.61 | 157.58 | H-Bond (Protein Donor) |
| OAQ | NE2 | HIS- 47 | 2.8 | 137.66 | H-Bond (Protein Donor) |
| CAA | CD1 | LEU- 50 | 4.05 | 0 | Hydrophobic |
| CAK | CD2 | LEU- 50 | 4.06 | 0 | Hydrophobic |
| CAF | CG1 | VAL- 139 | 3.66 | 0 | Hydrophobic |
| CAE | CG1 | VAL- 142 | 3.79 | 0 | Hydrophobic |
| CAE | CG2 | VAL- 143 | 3.88 | 0 | Hydrophobic |
| CA | CD | LYS- 160 | 4.15 | 0 | Hydrophobic |
| CAJ | CD | LYS- 160 | 3.89 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 184 | 4.13 | 0 | Hydrophobic |
| CAG | CG2 | THR- 186 | 4.33 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 187 | 4.45 | 0 | Hydrophobic |
| OAP | N | VAL- 187 | 3.31 | 164.03 | H-Bond (Protein Donor) |
