sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.030 Å
X-ray
2013-04-22
| Name: | Flavin-dependent thymidylate synthase |
|---|---|
| ID: | THYX_THEMA |
| AC: | Q9WYT0 |
| Organism: | Thermotoga maritima |
| Reign: | Bacteria |
| TaxID: | 243274 |
| EC Number: | 2.1.1.148 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| C | 34 % |
| D | 17 % |
| B-Factor: | 39.567 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.228 | 2561.625 |
| % Hydrophobic | % Polar |
|---|---|
| 28.59 | 71.41 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 63.76 % |
| 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 |
|---|---|---|
| 26.5846 | 45.2111 | 119.565 |
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 |
| C4' | CB | ARG- 78 | 3.89 | 0 | Hydrophobic |
| O4' | NE2 | HIS- 79 | 2.94 | 157.09 | H-Bond (Ligand Donor) |
| O2A | NE | ARG- 80 | 2.75 | 148.56 | H-Bond (Protein Donor) |
| O2A | NH2 | ARG- 80 | 3.43 | 124.7 | H-Bond (Protein Donor) |
| O2A | N | ARG- 80 | 2.91 | 157.87 | H-Bond (Protein Donor) |
| O1P | NH2 | ARG- 80 | 2.73 | 164.65 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 80 | 3.5 | 0 | Ionic (Protein Cationic) |
| O1P | CZ | ARG- 80 | 3.74 | 0 | Ionic (Protein Cationic) |
| O1A | N | ILE- 81 | 2.95 | 174.02 | H-Bond (Protein Donor) |
| C5B | CG1 | ILE- 81 | 3.55 | 0 | Hydrophobic |
| N1A | ND2 | ASN- 163 | 2.83 | 171.02 | H-Bond (Protein Donor) |
| O1P | NH1 | ARG- 165 | 3.36 | 137.03 | H-Bond (Protein Donor) |
| O2P | ND2 | ASN- 169 | 2.98 | 176.22 | H-Bond (Protein Donor) |
| C4' | CD1 | LEU- 173 | 4.08 | 0 | Hydrophobic |
| C4B | C1B | FAD- 301 | 3.81 | 0 | Hydrophobic |
| C1B | C4B | FAD- 301 | 3.75 | 0 | Hydrophobic |
| O3B | O3B | FAD- 301 | 2.85 | 147.46 | H-Bond (Ligand Donor) |
