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
2008-06-05
| Name: | D-3-phosphoglycerate dehydrogenase |
|---|---|
| ID: | SERA_MYCTU |
| AC: | P9WNX3 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 1.1.1.95 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 5 % |
| B | 95 % |
| B-Factor: | 41.549 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.547 | 1134.000 |
| % Hydrophobic | % Polar |
|---|---|
| 33.63 | 66.37 |
| According to VolSite | |
| HET Code: | HPV |
|---|---|
| Formula: | C3H2O7P |
| Molecular weight: | 181.018 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.31 % |
| Polar Surface area: | 139.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 0 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 16.5595 | 47.1706 | -18.9496 |
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 |
| O2P | OG | SER- 52 | 3.16 | 162.59 | H-Bond (Protein Donor) |
| O3 | N | VAL- 75 | 3.3 | 123.21 | H-Bond (Protein Donor) |
| O1 | N | VAL- 75 | 3.45 | 157.72 | H-Bond (Protein Donor) |
| O3 | N | GLY- 76 | 2.98 | 162.36 | H-Bond (Protein Donor) |
| O4P | NH1 | ARG- 132 | 3.23 | 154.74 | H-Bond (Protein Donor) |
