sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 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: | 43.812 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.036 | 1086.750 |
| % Hydrophobic | % Polar |
|---|---|
| 49.07 | 50.93 |
| According to VolSite | |
| HET Code: | ZVS |
|---|---|
| Formula: | C21H20F4N4O2S |
| Molecular weight: | 468.468 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.57 % |
| Polar Surface area: | 94.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -9.70153 | -57.2626 | -16.5913 |
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 |
| CAK | CG2 | VAL- 99 | 4.48 | 0 | Hydrophobic |
| FAE | CG1 | VAL- 99 | 3.73 | 0 | Hydrophobic |
| CAM | CG1 | VAL- 99 | 3.89 | 0 | Hydrophobic |
| FAD | CB | ALA- 100 | 3.32 | 0 | Hydrophobic |
| CAI | CB | ASP- 129 | 4.47 | 0 | Hydrophobic |
| CAH | CD1 | LEU- 132 | 4.47 | 0 | Hydrophobic |
| CAA | CB | LYS- 147 | 4.33 | 0 | Hydrophobic |
| CAB | CE1 | TYR- 182 | 3.39 | 0 | Hydrophobic |
| CAH | CD2 | LEU- 203 | 3.93 | 0 | Hydrophobic |
| NAR | OH | TYR- 235 | 2.78 | 170.02 | H-Bond (Protein Donor) |
| FAD | CD1 | TYR- 235 | 3.67 | 0 | Hydrophobic |
| CAX | CG | ARG- 238 | 4.08 | 0 | Hydrophobic |
| FAD | CD | ARG- 238 | 3.61 | 0 | Hydrophobic |
| CAL | CB | ARG- 238 | 4.07 | 0 | Hydrophobic |
| SAV | CE2 | PHE- 239 | 3.98 | 0 | Hydrophobic |
| CAP | CD2 | PHE- 239 | 4.24 | 0 | Hydrophobic |
| CAN | CB | PHE- 239 | 4.44 | 0 | Hydrophobic |
| CAP | SD | MET- 242 | 4.1 | 0 | Hydrophobic |
| CAY | SD | MET- 242 | 3.78 | 0 | Hydrophobic |
| CAX | CE | MET- 242 | 3.75 | 0 | Hydrophobic |
| CAP | CZ | PHE- 247 | 3.62 | 0 | Hydrophobic |
| CAB | CZ | PHE- 254 | 3.35 | 0 | Hydrophobic |
| CAQ | CE2 | PHE- 254 | 3.87 | 0 | Hydrophobic |
| SAV | CD1 | ILE- 272 | 3.85 | 0 | Hydrophobic |
| CAA | CG2 | ILE- 276 | 3.47 | 0 | Hydrophobic |
| NAS | ND2 | ASN- 277 | 3.06 | 158.29 | H-Bond (Protein Donor) |
