sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2004-07-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.570 | 4.570 | 4.570 | 0.000 | 4.570 | 6 |
| Name: | Thymidylate kinase |
|---|---|
| ID: | KTHY_MYCTU |
| AC: | P9WKE1 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 2.7.4.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 25.876 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.134 | 286.875 |
| % Hydrophobic | % Polar |
|---|---|
| 48.24 | 51.76 |
| According to VolSite | |
| HET Code: | THM |
|---|---|
| Formula: | C10H14N2O5 |
| Molecular weight: | 242.229 g/mol |
| DrugBank ID: | DB04485 |
| Buried Surface Area: | 77.42 % |
| Polar Surface area: | 99.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 34.5539 | 32.1633 | 59.9042 |
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 |
| O3' | OD2 | ASP- 9 | 2.92 | 148.74 | H-Bond (Ligand Donor) |
| C5M | CB | PHE- 36 | 3.97 | 0 | Hydrophobic |
| C5' | CG | PRO- 37 | 3.88 | 0 | Hydrophobic |
| C5M | CG | PRO- 37 | 4 | 0 | Hydrophobic |
| C5' | CZ | TYR- 39 | 4.46 | 0 | Hydrophobic |
| C4' | CD1 | LEU- 52 | 4 | 0 | Hydrophobic |
| C4' | CZ | PHE- 70 | 4.41 | 0 | Hydrophobic |
| C1' | CZ | PHE- 70 | 4.22 | 0 | Hydrophobic |
| C5M | CD2 | PHE- 70 | 4.37 | 0 | Hydrophobic |
| O4 | NH1 | ARG- 74 | 2.84 | 141.6 | H-Bond (Protein Donor) |
| O4 | NH2 | ARG- 74 | 2.89 | 139.28 | H-Bond (Protein Donor) |
| C2' | CD | ARG- 95 | 4.4 | 0 | Hydrophobic |
| C5M | CD | ARG- 95 | 4.1 | 0 | Hydrophobic |
| C5M | CB | SER- 99 | 4.2 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 100 | 2.98 | 151.05 | H-Bond (Ligand Donor) |
| C2' | CE1 | TYR- 103 | 3.71 | 0 | Hydrophobic |
| C1' | CD1 | TYR- 103 | 4.18 | 0 | Hydrophobic |
| C1' | CD2 | TYR- 165 | 3.8 | 0 | Hydrophobic |
