sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2001-04-20
| Name: | Glyceraldehyde-3-phosphate dehydrogenase |
|---|---|
| ID: | G3P_PANVR |
| AC: | P56649 |
| Organism: | Panulirus versicolor |
| Reign: | Eukaryota |
| TaxID: | 150436 |
| EC Number: | 1.2.1.12 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 10 % |
| C | 90 % |
| B-Factor: | 38.614 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.872 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.50 | 55.50 |
| According to VolSite | |
| HET Code: | APR |
|---|---|
| Formula: | C15H21N5O14P2 |
| Molecular weight: | 557.300 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.73 % |
| Polar Surface area: | 316.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 50.5261 | -8.30192 | 34.1938 |
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 |
| C1D | CG | ARG- 10 | 3.78 | 0 | Hydrophobic |
| C4D | CB | ARG- 10 | 4.24 | 0 | Hydrophobic |
| O2B | N | ILE- 11 | 3.14 | 143.61 | H-Bond (Protein Donor) |
| C5D | CD1 | ILE- 11 | 3.87 | 0 | Hydrophobic |
| C4D | CG1 | ILE- 11 | 3.99 | 0 | Hydrophobic |
| O2' | OD2 | ASP- 32 | 3.18 | 148.65 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 32 | 2.89 | 141.84 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 32 | 3.33 | 156.61 | H-Bond (Ligand Donor) |
| C2' | CD1 | PHE- 34 | 4.23 | 0 | Hydrophobic |
| N6 | O | MET- 77 | 3.11 | 137.84 | H-Bond (Ligand Donor) |
| C2D | CB | THR- 179 | 4 | 0 | Hydrophobic |
| O1D | N | ALA- 180 | 3.38 | 127.92 | H-Bond (Protein Donor) |
| O2D | N | ALA- 180 | 3.27 | 146.97 | H-Bond (Protein Donor) |
| C2D | CB | ALA- 180 | 4.11 | 0 | Hydrophobic |
