sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
2000-02-25
| Name: | Retinol-binding protein 2 |
|---|---|
| ID: | RET2_RAT |
| AC: | P06768 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 10.000 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.363 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 65.87 | 34.13 |
| According to VolSite | |
| HET Code: | RTL |
|---|---|
| Formula: | C20H30O |
| Molecular weight: | 286.452 g/mol |
| DrugBank ID: | DB00162 |
| Buried Surface Area: | 63.22 % |
| Polar Surface area: | 20.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 50.4863 | 55.2071 | 58.1617 |
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 |
| C18 | CZ | TYR- 20 | 3.68 | 0 | Hydrophobic |
| C19 | CZ | TYR- 20 | 3.56 | 0 | Hydrophobic |
| C4 | CG2 | THR- 30 | 4.19 | 0 | Hydrophobic |
| O1 | NZ | LYS- 41 | 3.02 | 171.32 | H-Bond (Protein Donor) |
| C15 | CG2 | THR- 52 | 3.97 | 0 | Hydrophobic |
| C16 | CG2 | THR- 54 | 3.52 | 0 | Hydrophobic |
| C2 | CB | SER- 56 | 3.63 | 0 | Hydrophobic |
| C3 | CB | PHE- 58 | 4.28 | 0 | Hydrophobic |
| C4 | CG | ARG- 59 | 4.14 | 0 | Hydrophobic |
| C17 | CB | ARG- 59 | 3.68 | 0 | Hydrophobic |
| C3 | CB | ARG- 59 | 3.76 | 0 | Hydrophobic |
| C17 | CG | TYR- 61 | 4.13 | 0 | Hydrophobic |
| C16 | CB | TYR- 61 | 3.99 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 78 | 3.98 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 78 | 3.47 | 0 | Hydrophobic |
| C15 | CH2 | TRP- 107 | 3.2 | 0 | Hydrophobic |
| C20 | CE2 | TRP- 107 | 3.34 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 120 | 4.37 | 0 | Hydrophobic |
