sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2010-02-18
| 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: | 30.568 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | NA |
| Ligandability | Volume (Å3) |
|---|---|
| 1.039 | 1096.875 |
| % Hydrophobic | % Polar |
|---|---|
| 48.92 | 51.08 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 49.01 % |
| Polar Surface area: | 276.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -42.0187 | 30.8499 | -2.07154 |
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 |
| O1B | N | ALA- 100 | 3.21 | 120.56 | H-Bond (Protein Donor) |
| O2A | N | ALA- 100 | 2.72 | 137.21 | H-Bond (Protein Donor) |
| O1B | N | GLY- 102 | 3.39 | 149.63 | H-Bond (Protein Donor) |
| O3B | N | GLY- 102 | 3.14 | 121.59 | H-Bond (Protein Donor) |
| O3B | N | LYS- 103 | 2.64 | 151.79 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 103 | 2.79 | 158.66 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 103 | 2.79 | 0 | Ionic (Protein Cationic) |
| O2B | OG | SER- 104 | 2.65 | 150.18 | H-Bond (Protein Donor) |
| O2B | N | SER- 104 | 2.72 | 152.35 | H-Bond (Protein Donor) |
| C3' | CB | SER- 104 | 4.47 | 0 | Hydrophobic |
| O1B | NH1 | ARG- 238 | 3.17 | 139.59 | H-Bond (Protein Donor) |
| O2A | NH1 | ARG- 238 | 2.98 | 137.38 | H-Bond (Protein Donor) |
| O2A | NH2 | ARG- 238 | 2.8 | 146.78 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 238 | 3.3 | 0 | Ionic (Protein Cationic) |
| C1' | CE | MET- 242 | 4.44 | 0 | Hydrophobic |
| O2' | O | HOH- 338 | 3.28 | 166.7 | H-Bond (Ligand Donor) |
| O3' | O | HOH- 490 | 2.51 | 149.2 | H-Bond (Protein Donor) |
