sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.270 Å
X-ray
2014-03-15
| Name: | Flavin-dependent thymidylate synthase |
|---|---|
| ID: | C1IC19_STRCI |
| AC: | C1IC19 |
| Organism: | Streptomyces cacaoi subsp. asoensis |
| Reign: | Bacteria |
| TaxID: | 249586 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 27 % |
| B | 31 % |
| C | 2 % |
| D | 41 % |
| B-Factor: | 26.037 |
|---|---|
| Number of residues: | 51 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 2 |
| Cofactors: | FAD FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.326 | 2143.125 |
| % Hydrophobic | % Polar |
|---|---|
| 36.54 | 63.46 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 66.12 % |
| 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 |
|---|---|---|
| -38.2453 | 4.98596 | 17.8425 |
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 |
| N3 | OG | SER- 33 | 2.92 | 130.23 | H-Bond (Ligand Donor) |
| C2' | CB | SER- 63 | 4.43 | 0 | Hydrophobic |
| O2' | OG | SER- 63 | 2.64 | 169.98 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 86 | 2.94 | 163.41 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 86 | 3.48 | 134.41 | H-Bond (Protein Donor) |
| C4' | CB | ARG- 86 | 3.95 | 0 | Hydrophobic |
| O2A | CZ | ARG- 88 | 3.11 | 0 | Ionic (Protein Cationic) |
| O2A | N | ARG- 88 | 3.18 | 158.08 | H-Bond (Protein Donor) |
| O2A | NH2 | ARG- 88 | 3.05 | 123.2 | H-Bond (Protein Donor) |
| O1P | NH2 | ARG- 88 | 3.17 | 120.15 | H-Bond (Protein Donor) |
| O1A | N | THR- 89 | 3.41 | 139.45 | H-Bond (Protein Donor) |
| O2 | N | GLU- 94 | 2.85 | 147.1 | H-Bond (Protein Donor) |
| N3 | O | GLU- 94 | 3.32 | 141.61 | H-Bond (Ligand Donor) |
| N1A | ND2 | ASN- 182 | 3.14 | 160.69 | H-Bond (Protein Donor) |
| C2B | CD | ARG- 184 | 4.38 | 0 | Hydrophobic |
| O1P | NH2 | ARG- 184 | 3.03 | 156.8 | H-Bond (Protein Donor) |
| O2P | NH2 | ARG- 184 | 3.3 | 124.04 | H-Bond (Protein Donor) |
| O2P | NH1 | ARG- 184 | 2.64 | 149.2 | H-Bond (Protein Donor) |
| O2P | CZ | ARG- 184 | 3.37 | 0 | Ionic (Protein Cationic) |
| C8M | CB | LEU- 192 | 3.98 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 192 | 4.21 | 0 | Hydrophobic |
| C8M | CD | ARG- 193 | 4.05 | 0 | Hydrophobic |
| C4B | C1B | FAD- 302 | 4.37 | 0 | Hydrophobic |
| C1B | C4B | FAD- 302 | 3.78 | 0 | Hydrophobic |
| O2' | O | HOH- 464 | 3.06 | 179.94 | H-Bond (Protein Donor) |
