sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2010-04-14
| Name: | Flavin-dependent thymidylate synthase |
|---|---|
| ID: | THYX_HELPY |
| AC: | O26061 |
| Organism: | Helicobacter pylori |
| Reign: | Bacteria |
| TaxID: | 85962 |
| EC Number: | 2.1.1.148 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 29 % |
| C | 36 % |
| D | 36 % |
| B-Factor: | 23.844 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | UMP FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.811 | 1717.875 |
| % Hydrophobic | % Polar |
|---|---|
| 36.15 | 63.85 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 74.19 % |
| Polar Surface area: | 381.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 7 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 35.4166 | 33.2825 | 47.1332 |
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 |
| O1A | O | HOH- 20 | 2.59 | 151.12 | H-Bond (Protein Donor) |
| O2' | O | ARG- 70 | 3.02 | 145.83 | H-Bond (Ligand Donor) |
| C7M | CD | ARG- 70 | 3.37 | 0 | Hydrophobic |
| C8 | CB | ARG- 70 | 4.08 | 0 | Hydrophobic |
| C4' | CB | SER- 73 | 3.87 | 0 | Hydrophobic |
| O2 | NH1 | ARG- 97 | 3.31 | 156.41 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 97 | 3.45 | 147.9 | H-Bond (Protein Donor) |
| C3' | CB | ARG- 97 | 4.22 | 0 | Hydrophobic |
| O2A | N | ARG- 99 | 2.74 | 125.95 | H-Bond (Protein Donor) |
| O2A | NH1 | ARG- 99 | 3.17 | 139.42 | H-Bond (Protein Donor) |
| C5B | CG1 | ILE- 100 | 3.25 | 0 | Hydrophobic |
| C4B | CD1 | ILE- 100 | 3.72 | 0 | Hydrophobic |
| C1B | CD1 | ILE- 100 | 4.49 | 0 | Hydrophobic |
| N3 | O | VAL- 105 | 2.92 | 143.63 | H-Bond (Ligand Donor) |
| N1A | ND2 | ASN- 186 | 2.71 | 161.97 | H-Bond (Protein Donor) |
| C2B | CD | ARG- 188 | 4.48 | 0 | Hydrophobic |
| O5' | NH1 | ARG- 188 | 3.13 | 169.46 | H-Bond (Protein Donor) |
| O1P | NH2 | ARG- 188 | 3.06 | 151.34 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 188 | 3.86 | 0 | Ionic (Protein Cationic) |
| O1P | ND2 | ASN- 192 | 3.39 | 148.11 | H-Bond (Protein Donor) |
| C8M | CB | LEU- 196 | 4.02 | 0 | Hydrophobic |
| C8M | CD | ARG- 197 | 4.19 | 0 | Hydrophobic |
| C7M | CB | LYS- 201 | 4.11 | 0 | Hydrophobic |
| C4B | C1B | FAD- 240 | 3.8 | 0 | Hydrophobic |
| C1B | C4B | FAD- 240 | 3.77 | 0 | Hydrophobic |
| C9A | C1' | UMP- 241 | 4.5 | 0 | Hydrophobic |
| C1' | C1' | UMP- 241 | 3.84 | 0 | Hydrophobic |
