sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.460 Å
X-ray
2007-03-24
| Name: | D-3-phosphoglycerate dehydrogenase |
|---|---|
| ID: | SERA_ECOLI |
| AC: | P0A9T0 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 1.1.1.95 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 2 % |
| B | 98 % |
| B-Factor: | 46.656 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.843 | 1657.125 |
| % Hydrophobic | % Polar |
|---|---|
| 35.03 | 64.97 |
| According to VolSite | |
| HET Code: | NAI |
|---|---|
| Formula: | C21H27N7O14P2 |
| Molecular weight: | 663.425 g/mol |
| DrugBank ID: | DB00157 |
| Buried Surface Area: | 68.18 % |
| Polar Surface area: | 342.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 19 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -9.95998 | 23.7858 | 9.11641 |
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 |
| C4N | CD1 | ILE- 84 | 4.38 | 0 | Hydrophobic |
| C4N | CG2 | VAL- 112 | 3.65 | 0 | Hydrophobic |
| O2A | N | HIS- 161 | 3.16 | 172.51 | H-Bond (Protein Donor) |
| O2N | N | ILE- 162 | 3.05 | 156.97 | H-Bond (Protein Donor) |
| C5D | CD1 | ILE- 162 | 4.21 | 0 | Hydrophobic |
| O3B | OD2 | ASP- 181 | 3.09 | 167.65 | H-Bond (Ligand Donor) |
| O3B | NZ | LYS- 185 | 2.61 | 161.12 | H-Bond (Protein Donor) |
| C5D | CB | HIS- 210 | 4.47 | 0 | Hydrophobic |
| O3D | O | VAL- 211 | 2.73 | 166.83 | H-Bond (Ligand Donor) |
| N6A | OG | SER- 216 | 3.02 | 125.02 | H-Bond (Ligand Donor) |
| N7N | O | ALA- 238 | 2.75 | 154.05 | H-Bond (Ligand Donor) |
| C4D | CB | SER- 239 | 4.38 | 0 | Hydrophobic |
| O3D | NE | ARG- 240 | 2.86 | 160.67 | H-Bond (Protein Donor) |
| C1D | CD | ARG- 240 | 4.43 | 0 | Hydrophobic |
| N7N | OD2 | ASP- 264 | 3.4 | 165.92 | H-Bond (Ligand Donor) |
