sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
1994-08-29
| Name: | Retinol-binding protein 4 |
|---|---|
| ID: | RET4_BOVIN |
| AC: | P18902 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.152 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.917 | 634.500 |
| % Hydrophobic | % Polar |
|---|---|
| 76.06 | 23.94 |
| According to VolSite | |
| HET Code: | FEN |
|---|---|
| Formula: | C26H33NO2 |
| Molecular weight: | 391.546 g/mol |
| DrugBank ID: | DB05076 |
| Buried Surface Area: | 63.84 % |
| Polar Surface area: | 49.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 34.2207 | 19.0609 | 50.8791 |
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 |
| C20 | CB | LEU- 35 | 4.29 | 0 | Hydrophobic |
| C6' | CG | LEU- 35 | 4.46 | 0 | Hydrophobic |
| C2' | CG | LEU- 35 | 3.61 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 36 | 3.3 | 0 | Hydrophobic |
| C20 | CD1 | PHE- 36 | 4.26 | 0 | Hydrophobic |
| C2 | CZ | PHE- 45 | 3.97 | 0 | Hydrophobic |
| C4 | CB | ALA- 55 | 3.78 | 0 | Hydrophobic |
| C17 | CB | ALA- 57 | 4.11 | 0 | Hydrophobic |
| C5 | CB | ALA- 57 | 3.69 | 0 | Hydrophobic |
| C2' | CG1 | VAL- 61 | 3.59 | 0 | Hydrophobic |
| C6' | CG1 | VAL- 61 | 4.35 | 0 | Hydrophobic |
| C3' | CB | LEU- 63 | 3.65 | 0 | Hydrophobic |
| C4' | CG | LEU- 63 | 3.47 | 0 | Hydrophobic |
| O4' | N | LEU- 64 | 3.21 | 149.95 | H-Bond (Protein Donor) |
| C18 | CB | MET- 73 | 3.8 | 0 | Hydrophobic |
| C3 | CZ | PHE- 77 | 3.61 | 0 | Hydrophobic |
| C1 | SD | MET- 88 | 4.37 | 0 | Hydrophobic |
| C6 | CE | MET- 88 | 3.54 | 0 | Hydrophobic |
| C16 | CE | MET- 88 | 4.38 | 0 | Hydrophobic |
| C18 | CE | MET- 88 | 4.27 | 0 | Hydrophobic |
| C3 | SD | MET- 88 | 3.68 | 0 | Hydrophobic |
| C18 | CB | TYR- 90 | 4.18 | 0 | Hydrophobic |
| O | N | GLN- 98 | 3.4 | 144.86 | H-Bond (Protein Donor) |
| C16 | CE2 | TYR- 133 | 4.18 | 0 | Hydrophobic |
| C19 | CZ | TYR- 133 | 4.15 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 135 | 4.13 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 135 | 4.13 | 0 | Hydrophobic |
