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
2002-11-25
| Name: | Glyceraldehyde-3-phosphate dehydrogenase |
|---|---|
| ID: | G3P_RABIT |
| AC: | P46406 |
| Organism: | Oryctolagus cuniculus |
| Reign: | Eukaryota |
| TaxID: | 9986 |
| EC Number: | 1.2.1.12 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| O | 8 % |
| R | 92 % |
| B-Factor: | 35.115 |
|---|---|
| Number of residues: | 49 |
| Including | |
| Standard Amino Acids: | 47 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.777 | 577.125 |
| % Hydrophobic | % Polar |
|---|---|
| 38.01 | 61.99 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.72 % |
| 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 |
|---|---|---|
| -9.74945 | -23.3109 | 8.84957 |
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 |
| O2A | N | ARG- 10 | 3.07 | 171.82 | H-Bond (Protein Donor) |
| O2N | N | ILE- 11 | 2.77 | 164.17 | H-Bond (Protein Donor) |
| C1D | CG1 | ILE- 11 | 4.41 | 0 | Hydrophobic |
| C4N | CD1 | ILE- 11 | 3.77 | 0 | Hydrophobic |
| C5D | CG1 | ILE- 11 | 4.3 | 0 | Hydrophobic |
| O3B | OD2 | ASP- 32 | 3.14 | 161.7 | H-Bond (Ligand Donor) |
| O2B | OD1 | ASP- 32 | 3.07 | 160.21 | H-Bond (Ligand Donor) |
| O2B | OD2 | ASP- 32 | 3.28 | 142.5 | H-Bond (Ligand Donor) |
| N6A | O | ARG- 77 | 3.39 | 156 | H-Bond (Ligand Donor) |
| C3D | CB | ALA- 120 | 4.45 | 0 | Hydrophobic |
| C1D | CB | ALA- 120 | 4.14 | 0 | Hydrophobic |
| C5N | CB | CSX- 149 | 3.33 | 0 | Hydrophobic |
| C6N | CE2 | TYR- 317 | 3.72 | 0 | Hydrophobic |
| C5N | CD2 | TYR- 317 | 3.58 | 0 | Hydrophobic |
