sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2016-01-29
| Name: | 2-dehydropantoate 2-reductase |
|---|---|
| ID: | Q5JGC2_THEKO |
| AC: | Q5JGC2 |
| Organism: | Thermococcus kodakarensis ) |
| Reign: | Archaea |
| TaxID: | 69014 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 39.106 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.522 | 1964.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.78 | 57.22 |
| According to VolSite | |
| HET Code: | NAP |
|---|---|
| Formula: | C21H25N7O17P3 |
| Molecular weight: | 740.381 g/mol |
| DrugBank ID: | DB03461 |
| Buried Surface Area: | 51.82 % |
| Polar Surface area: | 405.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 25.2282 | 40.7981 | 70.0402 |
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 |
| O3 | N | SER- 10 | 2.87 | 164.68 | H-Bond (Protein Donor) |
| C3N | CB | ILE- 11 | 4.1 | 0 | Hydrophobic |
| C4N | CD1 | ILE- 11 | 4.13 | 0 | Hydrophobic |
| O1X | CZ | ARG- 31 | 3.74 | 0 | Ionic (Protein Cationic) |
| O2X | CZ | ARG- 31 | 3.3 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 74 | 3.88 | 0 | Ionic (Protein Cationic) |
| C5D | CG | LYS- 74 | 3.82 | 0 | Hydrophobic |
| O3D | N | ASN- 100 | 3.24 | 150.27 | H-Bond (Protein Donor) |
| O2D | N | ASN- 100 | 3.4 | 138.96 | H-Bond (Protein Donor) |
| C2D | CB | ASN- 100 | 4.4 | 0 | Hydrophobic |
| C5N | CG2 | THR- 120 | 3.62 | 0 | Hydrophobic |
| O7N | N | ALA- 124 | 2.86 | 151.1 | H-Bond (Protein Donor) |
| N7N | O | ALA- 124 | 3.06 | 146.47 | H-Bond (Ligand Donor) |
| O3D | OE2 | GLU- 262 | 2.79 | 149.39 | H-Bond (Ligand Donor) |
| O2D | OE1 | GLU- 262 | 3.05 | 153.03 | H-Bond (Ligand Donor) |
| O3 | O | HOH- 534 | 3.01 | 180 | H-Bond (Protein Donor) |
