sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2011-09-02
| Name: | L-lactate dehydrogenase |
|---|---|
| ID: | LDH_THET8 |
| AC: | Q5SJA1 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 37.777 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.662 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 37.30 | 62.70 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 47.94 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 28.4624 | -19.6289 | 6.05156 |
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 |
| O2A | N | MET- 31 | 3.42 | 148.92 | H-Bond (Protein Donor) |
| O1B | N | VAL- 32 | 2.96 | 143.7 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 53 | 3.26 | 146.66 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 54 | 3.39 | 164.29 | H-Bond (Protein Donor) |
| O4' | N | GLY- 99 | 3.37 | 145.56 | H-Bond (Protein Donor) |
