sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2011-05-05
| Name: | UDP-N-acetylglucosamine 4-epimerase |
|---|---|
| ID: | GNE_PLESH |
| AC: | Q7BJX9 |
| Organism: | Plesiomonas shigelloides |
| Reign: | Bacteria |
| TaxID: | 703 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 98 % |
| B | 2 % |
| B-Factor: | 64.745 |
|---|---|
| Number of residues: | 52 |
| Including | |
| Standard Amino Acids: | 51 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.176 | 2598.750 |
| % Hydrophobic | % Polar |
|---|---|
| 40.78 | 59.22 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.22 % |
| 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 |
|---|---|---|
| 9.0168 | 30.9646 | -10.7678 |
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 |
| O1A | N | PHE- 27 | 2.85 | 173.51 | H-Bond (Protein Donor) |
| O1N | N | ILE- 28 | 2.88 | 165.79 | H-Bond (Protein Donor) |
| C5D | CB | ILE- 28 | 4.13 | 0 | Hydrophobic |
| C2B | CB | ASP- 47 | 3.98 | 0 | Hydrophobic |
| N6A | OD1 | ASP- 78 | 2.85 | 143.3 | H-Bond (Ligand Donor) |
| N1A | N | ILE- 79 | 3.02 | 167.76 | H-Bond (Protein Donor) |
| O3D | O | GLN- 98 | 2.97 | 128.09 | H-Bond (Ligand Donor) |
| C4D | CB | GLN- 98 | 3.97 | 0 | Hydrophobic |
| C1B | CB | ALA- 99 | 4.24 | 0 | Hydrophobic |
| C3D | CB | ALA- 100 | 3.99 | 0 | Hydrophobic |
| C4D | CB | ALA- 140 | 3.98 | 0 | Hydrophobic |
| C5N | CB | SER- 142 | 3.8 | 0 | Hydrophobic |
| O3D | NZ | LYS- 170 | 3.14 | 152.75 | H-Bond (Protein Donor) |
| O2D | NZ | LYS- 170 | 3.38 | 141.3 | H-Bond (Protein Donor) |
| C4N | CB | TYR- 193 | 3.73 | 0 | Hydrophobic |
| O7N | N | VAL- 196 | 3.4 | 156.24 | H-Bond (Protein Donor) |
