sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2012-03-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.190 | 5.190 | 5.190 | 0.000 | 5.190 | 1 |
| Name: | Thymidylate synthase |
|---|---|
| ID: | TYSY_MOUSE |
| AC: | P07607 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 2.1.1.45 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 89 % |
| F | 11 % |
| B-Factor: | 34.365 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.074 | 583.875 |
| % Hydrophobic | % Polar |
|---|---|
| 35.26 | 64.74 |
| According to VolSite | |
| HET Code: | UMP |
|---|---|
| Formula: | C9H11N2O8P |
| Molecular weight: | 306.166 g/mol |
| DrugBank ID: | DB03800 |
| Buried Surface Area: | 66.42 % |
| 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 |
|---|---|---|
| 76.1805 | -23.9799 | -49.7909 |
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 |
| O5' | NH2 | ARG- 44 | 2.89 | 147.09 | H-Bond (Protein Donor) |
| OP1 | NE | ARG- 44 | 2.7 | 169.98 | H-Bond (Protein Donor) |
| OP1 | CZ | ARG- 44 | 3.54 | 0 | Ionic (Protein Cationic) |
| O5' | NH2 | ARG- 169 | 3.42 | 140.87 | H-Bond (Protein Donor) |
| OP1 | NE | ARG- 169 | 3.34 | 140.06 | H-Bond (Protein Donor) |
| OP1 | NH2 | ARG- 169 | 3 | 152.7 | H-Bond (Protein Donor) |
| OP3 | NE | ARG- 169 | 3.12 | 149.04 | H-Bond (Protein Donor) |
| OP1 | CZ | ARG- 169 | 3.62 | 0 | Ionic (Protein Cationic) |
| OP3 | CZ | ARG- 169 | 3.92 | 0 | Ionic (Protein Cationic) |
| OP1 | CZ | ARG- 170 | 3.98 | 0 | Ionic (Protein Cationic) |
| OP2 | CZ | ARG- 170 | 3.18 | 0 | Ionic (Protein Cationic) |
| OP2 | NE | ARG- 170 | 2.63 | 148.27 | H-Bond (Protein Donor) |
| OP2 | NH2 | ARG- 170 | 2.87 | 134.9 | H-Bond (Protein Donor) |
| C5' | SG | CYS- 189 | 4.07 | 0 | Hydrophobic |
| C2' | SG | CYS- 189 | 4.14 | 0 | Hydrophobic |
| OP2 | NH2 | ARG- 209 | 2.87 | 152.4 | H-Bond (Protein Donor) |
| OP2 | NH1 | ARG- 209 | 3.38 | 131.51 | H-Bond (Protein Donor) |
| OP3 | NH1 | ARG- 209 | 2.89 | 156.76 | H-Bond (Protein Donor) |
| OP2 | CZ | ARG- 209 | 3.56 | 0 | Ionic (Protein Cationic) |
| OP3 | CZ | ARG- 209 | 3.76 | 0 | Ionic (Protein Cationic) |
| C2' | CB | SER- 210 | 4.12 | 0 | Hydrophobic |
| OP3 | OG | SER- 210 | 2.81 | 153.86 | H-Bond (Protein Donor) |
| O2 | N | ASP- 212 | 3.04 | 149.62 | H-Bond (Protein Donor) |
| C1' | CB | ASP- 212 | 3.82 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 220 | 2.85 | 173.12 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 220 | 3.07 | 130.94 | H-Bond (Protein Donor) |
| O3' | NE2 | HIS- 250 | 2.63 | 162.27 | H-Bond (Ligand Donor) |
| O3' | OH | TYR- 252 | 2.88 | 157.32 | H-Bond (Protein Donor) |
