sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2008-02-18
| Name: | Thiamine-monophosphate kinase |
|---|---|
| ID: | THIL_AQUAE |
| AC: | O67883 |
| Organism: | Aquifex aeolicus |
| Reign: | Bacteria |
| TaxID: | 224324 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 25 % |
| B | 75 % |
| B-Factor: | 52.361 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 4 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.221 | 877.500 |
| % Hydrophobic | % Polar |
|---|---|
| 34.62 | 65.38 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 67.2 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 31.0898 | 68.5421 | 123.325 |
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 |
| C1' | CG2 | ILE- 12 | 4.14 | 0 | Hydrophobic |
| C5' | CD1 | ILE- 12 | 3.98 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 24 | 3.8 | 0 | Hydrophobic |
| O3' | N | GLY- 25 | 2.93 | 163.12 | H-Bond (Protein Donor) |
| O3' | O | ASP- 26 | 2.92 | 136.91 | H-Bond (Ligand Donor) |
| N6 | OH | TYR- 101 | 2.77 | 139.47 | H-Bond (Ligand Donor) |
| O2' | N | GLY- 118 | 2.96 | 162.82 | H-Bond (Protein Donor) |
| N6 | O | ASN- 119 | 3.4 | 140.27 | H-Bond (Ligand Donor) |
| O2B | CZ | ARG- 142 | 4 | 0 | Ionic (Protein Cationic) |
| O1G | OG | SER- 209 | 2.97 | 145.28 | H-Bond (Protein Donor) |
| O3G | MG | MG- 309 | 2.28 | 0 | Metal Acceptor |
| O2B | MG | MG- 309 | 2.39 | 0 | Metal Acceptor |
| O2G | MG | MG- 310 | 2.45 | 0 | Metal Acceptor |
| O3G | MG | MG- 310 | 2.55 | 0 | Metal Acceptor |
| O1B | MG | MG- 310 | 2.77 | 0 | Metal Acceptor |
| O2G | MG | MG- 311 | 2.37 | 0 | Metal Acceptor |
| O1A | MG | MG- 311 | 2.34 | 0 | Metal Acceptor |
| O1G | MG | MG- 312 | 2.24 | 0 | Metal Acceptor |
| O3' | O | HOH- 315 | 3.19 | 123.38 | H-Bond (Ligand Donor) |
| O1A | O | HOH- 328 | 3.1 | 179.95 | H-Bond (Protein Donor) |
