sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.380 Å
X-ray
2002-01-08
| Name: | Cellular retinol-binding protein type II |
|---|---|
| ID: | Q8UVG6_DANRE |
| AC: | Q8UVG6 |
| Organism: | Danio rerio |
| Reign: | Eukaryota |
| TaxID: | 7955 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.628 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.348 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 66.89 | 33.11 |
| According to VolSite | |
| HET Code: | RTL |
|---|---|
| Formula: | C20H30O |
| Molecular weight: | 286.452 g/mol |
| DrugBank ID: | DB00162 |
| Buried Surface Area: | 65.53 % |
| 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 |
|---|---|---|
| 14.1922 | 55.5868 | 3.00838 |
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 | PHE- 16 | 3.57 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 16 | 4.11 | 0 | Hydrophobic |
| C18 | SD | MET- 20 | 3.9 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 25 | 4 | 0 | Hydrophobic |
| C4 | CB | ALA- 33 | 4.01 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 36 | 4.25 | 0 | Hydrophobic |
| C17 | CG | GLN- 38 | 4.24 | 0 | Hydrophobic |
| C17 | CG2 | THR- 53 | 4.5 | 0 | Hydrophobic |
| C17 | CB | SER- 55 | 4.3 | 0 | Hydrophobic |
| C3 | CD2 | PHE- 57 | 3.79 | 0 | Hydrophobic |
| C2 | CB | ARG- 58 | 3.94 | 0 | Hydrophobic |
| C3 | CD | ARG- 58 | 3.77 | 0 | Hydrophobic |
| C16 | CB | ARG- 58 | 4.24 | 0 | Hydrophobic |
| C16 | CB | TYR- 60 | 4.15 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 62 | 3.81 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 77 | 4.49 | 0 | Hydrophobic |
| C18 | CG | LEU- 77 | 3.85 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 77 | 3.79 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 77 | 3.5 | 0 | Hydrophobic |
| C14 | CE2 | TRP- 106 | 4.49 | 0 | Hydrophobic |
| C20 | CD2 | TRP- 106 | 3.64 | 0 | Hydrophobic |
| O1 | OE1 | GLN- 108 | 3 | 124.84 | H-Bond (Ligand Donor) |
| C11 | CD2 | LEU- 117 | 4.46 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 117 | 3.86 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 119 | 4.22 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 119 | 3.95 | 0 | Hydrophobic |
