sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
1999-02-22
| Name: | Cellular retinoic acid-binding protein 1 |
|---|---|
| ID: | RABP1_BOVIN |
| AC: | P62964 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.274 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.291 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 57.24 | 42.76 |
| According to VolSite | |
| HET Code: | A80 |
|---|---|
| Formula: | C22H24NO3 |
| Molecular weight: | 350.431 g/mol |
| DrugBank ID: | DB04942 |
| Buried Surface Area: | 58.14 % |
| Polar Surface area: | 69.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 25.5759 | 80.4379 | 7.78188 |
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 | CG1 | VAL- 24 | 3.94 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 28 | 3.96 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 28 | 4.45 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 31 | 3.76 | 0 | Hydrophobic |
| C20 | CB | ALA- 32 | 4.34 | 0 | Hydrophobic |
| C10 | CB | ALA- 32 | 4.12 | 0 | Hydrophobic |
| C18 | CB | ALA- 36 | 4.03 | 0 | Hydrophobic |
| C17 | CB | PRO- 39 | 3.84 | 0 | Hydrophobic |
| C17 | CG2 | THR- 54 | 3.38 | 0 | Hydrophobic |
| C18 | CG2 | THR- 56 | 3.51 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 58 | 4.47 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 58 | 3.55 | 0 | Hydrophobic |
| C7 | CD | ARG- 59 | 3.56 | 0 | Hydrophobic |
| O26 | NH2 | ARG- 131 | 3.22 | 130.38 | H-Bond (Protein Donor) |
| O26 | NE | ARG- 131 | 2.72 | 153.83 | H-Bond (Protein Donor) |
| O26 | CZ | ARG- 131 | 3.39 | 0 | Ionic (Protein Cationic) |
| N11 | O | HOH- 306 | 2.88 | 127.93 | H-Bond (Ligand Donor) |
