sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.030 Å
X-ray
2008-03-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.520 | 6.520 | 6.520 | 0.000 | 6.520 | 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 |
|---|---|
| B | 100 % |
| B-Factor: | 35.575 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.766 | 988.875 |
| % Hydrophobic | % Polar |
|---|---|
| 41.30 | 58.70 |
| According to VolSite | |
| HET Code: | 53H |
|---|---|
| Formula: | C16H25N7O7S |
| Molecular weight: | 459.477 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.51 % |
| Polar Surface area: | 229.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 0.794677 | -9.83687 | 35.6002 |
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 |
| C9 | CB | PRO- 38 | 4.35 | 0 | Hydrophobic |
| C11 | CB | PRO- 38 | 4.01 | 0 | Hydrophobic |
| C25 | CB | THR- 39 | 4.13 | 0 | Hydrophobic |
| C11 | CG | MET- 40 | 4.1 | 0 | Hydrophobic |
| O2A | N | MET- 40 | 2.98 | 157.71 | H-Bond (Protein Donor) |
| C21 | CD2 | LEU- 50 | 3.91 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 50 | 3.67 | 0 | Hydrophobic |
| N4 | OE1 | GLN- 72 | 3.02 | 141 | H-Bond (Ligand Donor) |
| C10 | CG1 | VAL- 139 | 4.33 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 142 | 3.95 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 143 | 4.44 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 143 | 4.36 | 0 | Hydrophobic |
| C9 | CE1 | PHE- 157 | 3.63 | 0 | Hydrophobic |
| O2 | N | GLY- 158 | 3.32 | 123.6 | H-Bond (Protein Donor) |
| O3 | N | GLY- 158 | 2.99 | 166.18 | H-Bond (Protein Donor) |
| O2 | OD2 | ASP- 161 | 2.61 | 159.11 | H-Bond (Ligand Donor) |
| O1 | NE2 | GLN- 164 | 3.31 | 158.59 | H-Bond (Protein Donor) |
| N4 | OE1 | GLN- 164 | 2.76 | 139.02 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 187 | 2.85 | 172.47 | H-Bond (Protein Donor) |
| N6 | O | VAL- 187 | 3.15 | 173.65 | H-Bond (Ligand Donor) |
| N6 | O | MET- 195 | 2.78 | 154.56 | H-Bond (Ligand Donor) |
| O3 | O | HOH- 830 | 2.72 | 159.12 | H-Bond (Ligand Donor) |
