sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.740 Å
X-ray
2009-05-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.520 | 5.520 | 5.520 | 0.000 | 5.520 | 1 |
| Name: | Thymidylate synthase |
|---|---|
| ID: | TYSY_HUMAN |
| AC: | P04818 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1.45 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 87 % |
| B | 13 % |
| B-Factor: | 46.982 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.178 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 39.27 | 60.73 |
| According to VolSite | |
| HET Code: | UMP |
|---|---|
| Formula: | C9H11N2O8P |
| Molecular weight: | 306.166 g/mol |
| DrugBank ID: | DB03800 |
| Buried Surface Area: | 51.63 % |
| 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 |
|---|---|---|
| 24.2152 | -10.3955 | 101.83 |
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 |
| OP1 | NE | ARG- 175 | 3.42 | 163.98 | H-Bond (Protein Donor) |
| OP3 | NH2 | ARG- 175 | 3.08 | 141.13 | H-Bond (Protein Donor) |
| OP3 | NE | ARG- 175 | 3.32 | 135.17 | H-Bond (Protein Donor) |
| OP3 | CZ | ARG- 175 | 3.61 | 0 | Ionic (Protein Cationic) |
| OP2 | NH1 | ARG- 176 | 2.57 | 130.07 | H-Bond (Protein Donor) |
| OP2 | NE | ARG- 176 | 2.53 | 134.44 | H-Bond (Protein Donor) |
| OP2 | CZ | ARG- 176 | 2.92 | 0 | Ionic (Protein Cationic) |
| C1' | SG | CYS- 195 | 4.28 | 0 | Hydrophobic |
| OP1 | CZ | ARG- 215 | 3.41 | 0 | Ionic (Protein Cationic) |
| OP1 | NH2 | ARG- 215 | 3.29 | 126.31 | H-Bond (Protein Donor) |
| OP1 | NH1 | ARG- 215 | 2.71 | 148.95 | H-Bond (Protein Donor) |
| OP2 | NH2 | ARG- 215 | 3.28 | 165.08 | H-Bond (Protein Donor) |
| OP1 | OG | SER- 216 | 3.05 | 174.34 | H-Bond (Protein Donor) |
| C2' | CB | ASP- 218 | 3.59 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 226 | 3.08 | 143.79 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 226 | 2.6 | 138.81 | H-Bond (Protein Donor) |
| O3' | NE2 | HIS- 256 | 3.49 | 141.41 | H-Bond (Ligand Donor) |
