sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.460 Å
X-ray
2002-01-15
| 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: | 19.953 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.663 | 286.875 |
| % Hydrophobic | % Polar |
|---|---|
| 83.53 | 16.47 |
| According to VolSite | |
| HET Code: | RTL |
|---|---|
| Formula: | C20H30O |
| Molecular weight: | 286.452 g/mol |
| DrugBank ID: | DB00162 |
| Buried Surface Area: | 76.88 % |
| 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 |
|---|---|---|
| 31.9146 | 19.3263 | 47.5174 |
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 |
| C15 | CD1 | LEU- 35 | 4.34 | 0 | Hydrophobic |
| C20 | CB | LEU- 35 | 3.82 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 36 | 4.02 | 0 | Hydrophobic |
| C3 | CB | ALA- 43 | 4.04 | 0 | Hydrophobic |
| C3 | CZ | PHE- 45 | 3.93 | 0 | Hydrophobic |
| C3 | CB | ALA- 55 | 3.83 | 0 | Hydrophobic |
| C17 | CB | ALA- 57 | 4.4 | 0 | Hydrophobic |
| C4 | CB | ALA- 57 | 3.96 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 61 | 4.11 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 63 | 4.39 | 0 | Hydrophobic |
| C18 | CB | MET- 73 | 4 | 0 | Hydrophobic |
| C4 | SD | MET- 88 | 3.94 | 0 | Hydrophobic |
| C16 | CE | MET- 88 | 4.16 | 0 | Hydrophobic |
| C18 | SD | MET- 88 | 3.86 | 0 | Hydrophobic |
| C1 | SD | MET- 88 | 4.35 | 0 | Hydrophobic |
| C18 | CB | TYR- 90 | 3.66 | 0 | Hydrophobic |
| C19 | CE2 | TYR- 90 | 4.12 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 97 | 3.61 | 0 | Hydrophobic |
| C15 | CB | GLN- 98 | 4.21 | 0 | Hydrophobic |
| C20 | CB | GLN- 98 | 3.61 | 0 | Hydrophobic |
| O1 | N | GLN- 98 | 2.64 | 153.39 | H-Bond (Protein Donor) |
| C16 | CE2 | TYR- 133 | 4.1 | 0 | Hydrophobic |
| C19 | CZ | TYR- 133 | 4.32 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 135 | 4.04 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 135 | 3.79 | 0 | Hydrophobic |
| C2 | CZ | PHE- 137 | 4.48 | 0 | Hydrophobic |
| C17 | CZ | PHE- 137 | 4.36 | 0 | Hydrophobic |
