sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.270 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: | 37.270 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.895 | 921.375 |
| % Hydrophobic | % Polar |
|---|---|
| 51.65 | 48.35 |
| According to VolSite | |
| HET Code: | ZVW |
|---|---|
| Formula: | C27H23F5N4O2S |
| Molecular weight: | 562.554 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.42 % |
| Polar Surface area: | 94.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -18.5915 | -9.14577 | 11.1236 |
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 |
| C1 | CG1 | VAL- 99 | 4.04 | 0 | Hydrophobic |
| C34 | CG2 | VAL- 99 | 4.22 | 0 | Hydrophobic |
| F37 | CG1 | VAL- 99 | 3.41 | 0 | Hydrophobic |
| F7 | CB | ALA- 100 | 3.21 | 0 | Hydrophobic |
| C32 | CD1 | LEU- 132 | 3.9 | 0 | Hydrophobic |
| C31 | CG | LYS- 147 | 4.02 | 0 | Hydrophobic |
| C17 | CE1 | TYR- 182 | 3.36 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 203 | 3.65 | 0 | Hydrophobic |
| F7 | CD1 | TYR- 235 | 3.4 | 0 | Hydrophobic |
| C3 | CE1 | TYR- 235 | 3.16 | 0 | Hydrophobic |
| N13 | OH | TYR- 235 | 2.52 | 157.3 | H-Bond (Protein Donor) |
| N14 | OH | TYR- 235 | 3.39 | 138.28 | H-Bond (Protein Donor) |
| C3 | CB | ARG- 238 | 3.9 | 0 | Hydrophobic |
| F7 | CD | ARG- 238 | 3.33 | 0 | Hydrophobic |
| S11 | CE2 | PHE- 239 | 3.91 | 0 | Hydrophobic |
| C4 | CB | PHE- 239 | 4.03 | 0 | Hydrophobic |
| C9 | CE | MET- 242 | 4.12 | 0 | Hydrophobic |
| C5 | SD | MET- 242 | 3.62 | 0 | Hydrophobic |
| C4 | SD | MET- 242 | 3.69 | 0 | Hydrophobic |
| C10 | CE1 | PHE- 247 | 4.06 | 0 | Hydrophobic |
| C10 | CD2 | PHE- 254 | 3.64 | 0 | Hydrophobic |
| S11 | CE2 | PHE- 254 | 4.48 | 0 | Hydrophobic |
| C17 | CZ | PHE- 254 | 3.41 | 0 | Hydrophobic |
| S11 | CE2 | TYR- 257 | 4.25 | 0 | Hydrophobic |
| S11 | CD1 | ILE- 272 | 4.39 | 0 | Hydrophobic |
| C21 | CG1 | ILE- 272 | 4.34 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 272 | 3.79 | 0 | Hydrophobic |
| C26 | CG2 | ILE- 276 | 3.33 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 276 | 3.49 | 0 | Hydrophobic |
| N14 | ND2 | ASN- 277 | 3.09 | 171 | H-Bond (Protein Donor) |
