sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2002-11-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.350 | 5.350 | 5.350 | 0.000 | 5.350 | 1 |
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 21.364 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.117 | 600.750 |
| % Hydrophobic | % Polar |
|---|---|
| 33.71 | 66.29 |
| According to VolSite | |
| HET Code: | TMP |
|---|---|
| Formula: | C10H13N2O8P |
| Molecular weight: | 320.193 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.62 % |
| Polar Surface area: | 161.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 24.9218 | 11.4295 | 8.68738 |
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 |
| C5M | CB | PHE- 36 | 4.19 | 0 | Hydrophobic |
| C5' | CG | PRO- 37 | 4.24 | 0 | Hydrophobic |
| C5M | CG | PRO- 37 | 3.96 | 0 | Hydrophobic |
| O3P | OH | TYR- 39 | 2.7 | 166.08 | H-Bond (Protein Donor) |
| C4' | CD1 | LEU- 52 | 3.91 | 0 | Hydrophobic |
| C4' | CZ | PHE- 70 | 4.25 | 0 | Hydrophobic |
| C1' | CZ | PHE- 70 | 4.16 | 0 | Hydrophobic |
| C5M | CD1 | PHE- 70 | 4.28 | 0 | Hydrophobic |
| O4 | NH2 | ARG- 74 | 2.85 | 144.06 | H-Bond (Protein Donor) |
| O4 | NH1 | ARG- 74 | 2.87 | 142.95 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 95 | 3.83 | 0 | Ionic (Protein Cationic) |
| O1P | NE | ARG- 95 | 2.74 | 149.63 | H-Bond (Protein Donor) |
| C5M | CD | ARG- 95 | 3.68 | 0 | Hydrophobic |
| C5M | CB | SER- 99 | 4.09 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 100 | 3.07 | 155.13 | H-Bond (Ligand Donor) |
| C2' | CE1 | TYR- 103 | 3.96 | 0 | Hydrophobic |
| C1' | CD1 | TYR- 103 | 4.27 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 163 | 3.46 | 151.82 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 163 | 3.03 | 153.12 | H-Bond (Ligand Donor) |
| C1' | CD2 | TYR- 165 | 4.04 | 0 | Hydrophobic |
| O1P | O | HOH- 1014 | 2.92 | 179.97 | H-Bond (Protein Donor) |
