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
2013-03-22
| Name: | Pantothenate kinase |
|---|---|
| ID: | COAA_MYCTU |
| AC: | P9WPA7 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 2.7.1.33 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.622 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.907 | 853.875 |
| % Hydrophobic | % Polar |
|---|---|
| 50.59 | 49.41 |
| According to VolSite | |
| HET Code: | ZVZ |
|---|---|
| Formula: | C26H28N5O2 |
| Molecular weight: | 442.533 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.46 % |
| Polar Surface area: | 82.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -18.6133 | -7.10336 | 10.7271 |
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 |
| CAE | CD1 | LEU- 132 | 3.71 | 0 | Hydrophobic |
| CAS | CD | LYS- 147 | 3.84 | 0 | Hydrophobic |
| CAH | CG | LYS- 147 | 3.92 | 0 | Hydrophobic |
| NAW | OH | TYR- 182 | 2.55 | 149.41 | H-Bond (Ligand Donor) |
| CAS | CE1 | TYR- 182 | 4.35 | 0 | Hydrophobic |
| CAF | CD1 | LEU- 203 | 3.83 | 0 | Hydrophobic |
| CAT | CZ | TYR- 235 | 4.13 | 0 | Hydrophobic |
| CAT | CD2 | PHE- 239 | 3.49 | 0 | Hydrophobic |
| CAT | SD | MET- 242 | 3.87 | 0 | Hydrophobic |
| CAT | CZ | PHE- 247 | 4.11 | 0 | Hydrophobic |
| CBC | CG2 | ILE- 272 | 4.02 | 0 | Hydrophobic |
| CAN | CD1 | ILE- 272 | 4 | 0 | Hydrophobic |
| CAJ | CD1 | ILE- 276 | 3.25 | 0 | Hydrophobic |
| NBF | O | HOH- 2119 | 2.81 | 160.49 | H-Bond (Ligand Donor) |
