sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.730 Å
X-ray
2009-09-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.750 | 5.750 | 5.750 | 0.000 | 5.750 | 1 |
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 22.194 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.555 | 1076.625 |
| % Hydrophobic | % Polar |
|---|---|
| 34.80 | 65.20 |
| According to VolSite | |
| HET Code: | FG6 |
|---|---|
| Formula: | C20H15N2O7S |
| Molecular weight: | 427.407 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.69 % |
| Polar Surface area: | 139.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 15.048 | 10.3167 | 1.1056 |
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 |
| CAG | CB | PRO- 38 | 3.95 | 0 | Hydrophobic |
| OAD | N | MET- 40 | 2.73 | 164.51 | H-Bond (Protein Donor) |
| CAJ | CG | MET- 40 | 4.02 | 0 | Hydrophobic |
| O | NE2 | HIS- 44 | 2.81 | 173.12 | H-Bond (Protein Donor) |
| OAD | NE2 | HIS- 47 | 2.82 | 138.69 | H-Bond (Protein Donor) |
| CAA | CB | ALA- 49 | 3.98 | 0 | Hydrophobic |
| CAA | CD2 | LEU- 50 | 3.72 | 0 | Hydrophobic |
| CAM | CD2 | LEU- 50 | 4.25 | 0 | Hydrophobic |
| CAH | CG2 | VAL- 143 | 3.46 | 0 | Hydrophobic |
| CAK | CE1 | PHE- 157 | 3.11 | 0 | Hydrophobic |
| CA | CD | LYS- 160 | 3.57 | 0 | Hydrophobic |
| CAL | CB | LYS- 160 | 3.71 | 0 | Hydrophobic |
| OXT | NZ | LYS- 160 | 3.96 | 0 | Ionic (Protein Cationic) |
| CAH | CD1 | ILE- 168 | 4.43 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 184 | 3.79 | 0 | Hydrophobic |
| CAI | CG2 | THR- 186 | 4.04 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 187 | 3.67 | 0 | Hydrophobic |
| OAR | N | VAL- 187 | 3.1 | 158.58 | H-Bond (Protein Donor) |
| CAI | CB | MET- 195 | 4.16 | 0 | Hydrophobic |
| OXT | OG | SER- 196 | 2.78 | 163.73 | H-Bond (Protein Donor) |
| O | N | SER- 197 | 3.24 | 162.17 | H-Bond (Protein Donor) |
| OAR | O | HOH- 442 | 2.86 | 136.74 | H-Bond (Protein Donor) |
