sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2014-07-28
| Name: | Retinol-binding protein 2 |
|---|---|
| ID: | RET2_HUMAN |
| AC: | P50120 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.237 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.331 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 59.59 | 40.41 |
| According to VolSite | |
| HET Code: | RTL |
|---|---|
| Formula: | C20H30O |
| Molecular weight: | 286.452 g/mol |
| DrugBank ID: | DB00162 |
| Buried Surface Area: | 59.44 % |
| 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 |
|---|---|---|
| 26.0462 | 12.0901 | 34.7326 |
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 |
| C16 | CZ | PHE- 16 | 4.22 | 0 | Hydrophobic |
| C18 | CZ | PHE- 16 | 3.54 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 16 | 4.5 | 0 | Hydrophobic |
| C8 | CZ | PHE- 16 | 4.01 | 0 | Hydrophobic |
| C19 | CE2 | TYR- 19 | 3.93 | 0 | Hydrophobic |
| C4 | SD | MET- 20 | 4.43 | 0 | Hydrophobic |
| C18 | SD | MET- 20 | 3.76 | 0 | Hydrophobic |
| C4 | CB | ALA- 33 | 3.89 | 0 | Hydrophobic |
| C16 | CG | GLN- 38 | 4.38 | 0 | Hydrophobic |
| O1 | NZ | LYS- 40 | 3.07 | 147.14 | H-Bond (Protein Donor) |
| C2 | CB | ARG- 58 | 3.81 | 0 | Hydrophobic |
| C11 | CD2 | TYR- 60 | 4.15 | 0 | Hydrophobic |
| C17 | CB | TYR- 60 | 4.18 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 62 | 4.33 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 77 | 4.12 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 77 | 4.05 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 77 | 3.32 | 0 | Hydrophobic |
| C20 | CE2 | TRP- 106 | 3.72 | 0 | Hydrophobic |
| C15 | CZ2 | TRP- 106 | 3.93 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 117 | 3.78 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 119 | 4.28 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 119 | 4.04 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 119 | 3.77 | 0 | Hydrophobic |
