sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.280 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: | 40.798 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.931 | 904.500 |
| % Hydrophobic | % Polar |
|---|---|
| 57.84 | 42.16 |
| According to VolSite | |
| HET Code: | ZVU |
|---|---|
| Formula: | C20H18F4N4OS |
| Molecular weight: | 438.442 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.57 % |
| Polar Surface area: | 85.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -18.9133 | -10.5418 | 11.8479 |
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 |
| FAE | CG1 | VAL- 99 | 4.34 | 0 | Hydrophobic |
| FAF | CG1 | VAL- 99 | 3.86 | 0 | Hydrophobic |
| CAK | CG2 | VAL- 99 | 4.12 | 0 | Hydrophobic |
| FAD | CG1 | VAL- 99 | 3.51 | 0 | Hydrophobic |
| FAD | CB | ALA- 100 | 3.6 | 0 | Hydrophobic |
| CAJ | CD1 | LEU- 132 | 3.64 | 0 | Hydrophobic |
| CAJ | CG | LYS- 147 | 4.08 | 0 | Hydrophobic |
| CAA | CD | LYS- 147 | 3.66 | 0 | Hydrophobic |
| FAG | CE2 | TYR- 177 | 3.69 | 0 | Hydrophobic |
| OAC | OH | TYR- 177 | 2.59 | 133.53 | H-Bond (Protein Donor) |
| FAG | CD1 | TYR- 182 | 3.58 | 0 | Hydrophobic |
| CAB | CD1 | TYR- 182 | 3.81 | 0 | Hydrophobic |
| CAP | CZ | TYR- 182 | 3.55 | 0 | Hydrophobic |
| FAE | CE1 | TYR- 182 | 4.1 | 0 | Hydrophobic |
| CAI | CD1 | LEU- 203 | 3.8 | 0 | Hydrophobic |
| FAD | CD1 | TYR- 235 | 3.46 | 0 | Hydrophobic |
| CAM | CE1 | TYR- 235 | 3.36 | 0 | Hydrophobic |
| CAM | CB | ARG- 238 | 4.09 | 0 | Hydrophobic |
| FAD | CD | ARG- 238 | 3.75 | 0 | Hydrophobic |
| CAO | CB | PHE- 239 | 4.22 | 0 | Hydrophobic |
| SAT | CD1 | PHE- 239 | 3.93 | 0 | Hydrophobic |
| CAW | SD | MET- 242 | 3.9 | 0 | Hydrophobic |
| CAP | CZ | PHE- 247 | 4.34 | 0 | Hydrophobic |
| CAB | CZ | PHE- 254 | 3.76 | 0 | Hydrophobic |
| SAT | CE2 | PHE- 254 | 4.48 | 0 | Hydrophobic |
| SAT | CD1 | ILE- 272 | 4.01 | 0 | Hydrophobic |
| CAA | CD1 | ILE- 276 | 4.22 | 0 | Hydrophobic |
| NAR | ND2 | ASN- 277 | 3.01 | 166.55 | H-Bond (Protein Donor) |
| NAQ | ND2 | ASN- 277 | 3.38 | 134.18 | H-Bond (Protein Donor) |
| NAS | O | HOH- 2040 | 3.06 | 161.31 | H-Bond (Ligand Donor) |
