sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.690 Å
X-ray
2009-06-19
| Name: | Retinaldehyde-binding protein 1 |
|---|---|
| ID: | RLBP1_HUMAN |
| AC: | P12271 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.176 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 2.161 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 93.81 | 6.19 |
| According to VolSite | |
| HET Code: | RET |
|---|---|
| Formula: | C20H28O |
| Molecular weight: | 284.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.75 % |
| Polar Surface area: | 17.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 4.03095 | 4.92481 | 13.1023 |
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 | CZ | PHE- 161 | 3.97 | 0 | Hydrophobic |
| C20 | CH2 | TRP- 166 | 4.4 | 0 | Hydrophobic |
| C20 | CZ | PHE- 173 | 3.55 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 176 | 4.12 | 0 | Hydrophobic |
| O1 | OH | TYR- 180 | 2.84 | 156.06 | H-Bond (Protein Donor) |
| O1 | OE2 | GLU- 202 | 2.61 | 170.56 | H-Bond (Protein Donor) |
| C19 | CZ | PHE- 204 | 3.88 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 215 | 4.18 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 220 | 3.54 | 0 | Hydrophobic |
| C16 | CE | MET- 223 | 3.56 | 0 | Hydrophobic |
| C17 | CG | MET- 223 | 4.04 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 224 | 3.94 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 224 | 4 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 227 | 4.1 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 238 | 3.88 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 240 | 4.39 | 0 | Hydrophobic |
| C18 | CZ | PHE- 240 | 3.86 | 0 | Hydrophobic |
| C18 | CZ | PHE- 247 | 4.01 | 0 | Hydrophobic |
| C19 | CG2 | THR- 250 | 3.8 | 0 | Hydrophobic |
| C18 | CD1 | TYR- 251 | 4.12 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 254 | 4.25 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 254 | 3.97 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 258 | 4.21 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 258 | 3.96 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 266 | 3.84 | 0 | Hydrophobic |
