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
1975-07-01
| Name: | Glyceraldehyde-3-phosphate dehydrogenase |
|---|---|
| ID: | G3P_HOMAM |
| AC: | P00357 |
| Organism: | Homarus americanus |
| Reign: | Eukaryota |
| TaxID: | 6706 |
| EC Number: | 1.2.1.12 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| G | 4 % |
| R | 96 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.408 | 1248.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.30 | 52.70 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 46.93 % |
| 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 |
|---|---|---|
| 7.11705 | -10.1056 | 19.6719 |
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 |
| O3B | OD2 | ASP- 32 | 3.47 | 159.29 | H-Bond (Ligand Donor) |
| O3D | O | SER- 119 | 2.97 | 146.24 | H-Bond (Ligand Donor) |
| C1D | CB | SER- 119 | 3.83 | 0 | Hydrophobic |
| C2D | CB | ALA- 120 | 4.15 | 0 | Hydrophobic |
| C4N | CB | ASN- 313 | 4.28 | 0 | Hydrophobic |
| C4N | CD2 | TYR- 317 | 4.19 | 0 | Hydrophobic |
