sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.450 Å
X-ray
2009-06-23
| Name: | Flavin-dependent thymidylate synthase |
|---|---|
| ID: | THYX_MYCTU |
| AC: | P9WG57 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 2.1.1.148 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 38 % |
| B | 33 % |
| C | 28 % |
| B-Factor: | 31.155 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.508 | 1805.625 |
| % Hydrophobic | % Polar |
|---|---|
| 31.40 | 68.60 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 59.78 % |
| 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 |
|---|---|---|
| 17.6118 | 3.75196 | -15.5824 |
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 |
| C8 | CB | HIS- 69 | 4.14 | 0 | Hydrophobic |
| C1' | CB | SER- 71 | 3.94 | 0 | Hydrophobic |
| C4' | CB | SER- 71 | 4.42 | 0 | Hydrophobic |
| N1 | NH2 | ARG- 95 | 3.45 | 136.65 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 95 | 3.03 | 135.62 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 95 | 2.73 | 152.75 | H-Bond (Protein Donor) |
| C3' | CB | ARG- 95 | 4.2 | 0 | Hydrophobic |
| C5' | CB | ARG- 95 | 4.18 | 0 | Hydrophobic |
| O1A | ND1 | HIS- 96 | 2.79 | 168.04 | H-Bond (Protein Donor) |
| O2A | N | ARG- 97 | 2.73 | 158.6 | H-Bond (Protein Donor) |
| O2A | NE | ARG- 97 | 2.97 | 163.73 | H-Bond (Protein Donor) |
| O3P | NH2 | ARG- 97 | 3.34 | 172.32 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 97 | 3.74 | 0 | Ionic (Protein Cationic) |
| DuAr | DuAr | HIS- 98 | 3.86 | 0 | Aromatic Face/Face |
| O2 | N | GLN- 103 | 2.9 | 138.68 | H-Bond (Protein Donor) |
| N3 | O | GLN- 103 | 2.89 | 175.17 | H-Bond (Ligand Donor) |
| N1A | ND2 | ASN- 188 | 2.93 | 166.2 | H-Bond (Protein Donor) |
| O1P | NH2 | ARG- 190 | 3.36 | 139.66 | H-Bond (Protein Donor) |
| O1P | NH1 | ARG- 190 | 2.99 | 162.37 | H-Bond (Protein Donor) |
| O2P | NH2 | ARG- 190 | 3.34 | 156.11 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 190 | 3.64 | 0 | Ionic (Protein Cationic) |
| C4B | C1B | FAD- 501 | 3.99 | 0 | Hydrophobic |
| C1B | C4B | FAD- 501 | 3.81 | 0 | Hydrophobic |
| O3B | O3B | FAD- 501 | 3.34 | 123.56 | H-Bond (Protein Donor) |
| O2B | O3B | FAD- 501 | 3.39 | 164.15 | H-Bond (Protein Donor) |
