sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.220 Å
X-ray
2013-11-11
| Name: | D-3-phosphoglycerate dehydrogenase, putative |
|---|---|
| ID: | Q76KF5_ENTHI |
| AC: | Q76KF5 |
| Organism: | Entamoeba histolytica |
| Reign: | Eukaryota |
| TaxID: | 5759 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 39.348 |
|---|---|
| Number of residues: | 54 |
| Including | |
| Standard Amino Acids: | 50 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.390 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 44.12 | 55.88 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.82 % |
| 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 |
|---|---|---|
| -7.27825 | -21.1838 | -20.0059 |
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 |
| C3D | CB | ALA- 78 | 4.11 | 0 | Hydrophobic |
| C5N | CB | ALA- 78 | 4.1 | 0 | Hydrophobic |
| C5N | CG2 | VAL- 106 | 3.72 | 0 | Hydrophobic |
| C4N | CG2 | VAL- 106 | 3.8 | 0 | Hydrophobic |
| O2A | N | TYR- 142 | 3.09 | 173.68 | H-Bond (Protein Donor) |
| O2N | N | VAL- 143 | 3.04 | 162.36 | H-Bond (Protein Donor) |
| O3B | OD1 | ASP- 162 | 2.97 | 163.34 | H-Bond (Ligand Donor) |
| O2B | OD1 | ASP- 162 | 2.96 | 144.82 | H-Bond (Ligand Donor) |
| O2B | OD2 | ASP- 162 | 2.59 | 144.31 | H-Bond (Ligand Donor) |
| C2B | CD2 | PHE- 164 | 4.47 | 0 | Hydrophobic |
| C5D | CB | HIS- 187 | 4.32 | 0 | Hydrophobic |
| N7N | O | THR- 215 | 2.95 | 157.2 | H-Bond (Ligand Donor) |
| C4D | CB | ALA- 216 | 4.46 | 0 | Hydrophobic |
| N7N | OD2 | ASP- 241 | 3.09 | 159.33 | H-Bond (Ligand Donor) |
| O7N | NZ | LYS- 263 | 3.16 | 126.13 | H-Bond (Protein Donor) |
| O7N | N | ALA- 266 | 3.25 | 124.8 | H-Bond (Protein Donor) |
| O4D | O | HOH- 507 | 3.08 | 165.54 | H-Bond (Protein Donor) |
| O2D | O | HOH- 514 | 3.15 | 179.95 | H-Bond (Protein Donor) |
