sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2009-02-26
| Name: | L-threonine 3-dehydrogenase |
|---|---|
| ID: | TDH_THEKO |
| AC: | Q5JI69 |
| Organism: | Thermococcus kodakarensis ) |
| Reign: | Archaea |
| TaxID: | 69014 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 5 % |
| D | 95 % |
| B-Factor: | 30.744 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.132 | 1414.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.10 | 59.90 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.73 % |
| Polar Surface area: | 343.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -7.19461 | -44.6394 | -21.6121 |
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 |
| C5D | CB | LEU- 179 | 3.55 | 0 | Hydrophobic |
| C4D | CD1 | LEU- 179 | 3.53 | 0 | Hydrophobic |
| C5N | CD1 | LEU- 179 | 4.38 | 0 | Hydrophobic |
| O1N | N | GLY- 180 | 3.42 | 145.76 | H-Bond (Protein Donor) |
| O3B | OE1 | GLU- 199 | 3.3 | 171.1 | H-Bond (Ligand Donor) |
| C1B | CG | PRO- 200 | 3.76 | 0 | Hydrophobic |
| O2A | NH1 | ARG- 204 | 2.8 | 132.27 | H-Bond (Protein Donor) |
| O2A | NH2 | ARG- 204 | 2.9 | 128.28 | H-Bond (Protein Donor) |
| O5B | NH1 | ARG- 204 | 2.8 | 120.64 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 204 | 3.23 | 0 | Ionic (Protein Cationic) |
| C1B | CB | SER- 244 | 4.15 | 0 | Hydrophobic |
| C4B | CB | SER- 244 | 3.72 | 0 | Hydrophobic |
| N7N | O | LEU- 266 | 2.59 | 155.57 | H-Bond (Ligand Donor) |
| C3N | CD1 | LEU- 266 | 3.81 | 0 | Hydrophobic |
| C2D | CD1 | LEU- 268 | 4.44 | 0 | Hydrophobic |
| C3N | CD1 | LEU- 268 | 4.11 | 0 | Hydrophobic |
