sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2008-04-22
| Name: | Cellular retinoic acid-binding protein 2 |
|---|---|
| ID: | RABP2_HUMAN |
| AC: | P29373 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 16.246 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.339 | 722.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.41 | 41.59 |
| According to VolSite | |
| HET Code: | REA |
|---|---|
| Formula: | C20H27O2 |
| Molecular weight: | 299.427 g/mol |
| DrugBank ID: | DB00755 |
| Buried Surface Area: | 63.01 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 21.9206 | 24.6317 | 20.212 |
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 |
| C18 | CD2 | LEU- 19 | 3.7 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 24 | 4.21 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 28 | 3.97 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 31 | 3.87 | 0 | Hydrophobic |
| C18 | CB | ALA- 32 | 3.9 | 0 | Hydrophobic |
| C19 | CB | ALA- 32 | 4.42 | 0 | Hydrophobic |
| C17 | CB | ALA- 32 | 3.85 | 0 | Hydrophobic |
| C19 | CB | ALA- 35 | 4.4 | 0 | Hydrophobic |
| C19 | CB | ALA- 36 | 3.85 | 0 | Hydrophobic |
| C20 | CB | ALA- 36 | 4.41 | 0 | Hydrophobic |
| C20 | CB | PRO- 39 | 3.76 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 54 | 3.85 | 0 | Hydrophobic |
| C19 | CG2 | THR- 56 | 4.39 | 0 | Hydrophobic |
| C20 | CG2 | THR- 56 | 4.3 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 58 | 3.91 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 58 | 4.22 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 58 | 3.64 | 0 | Hydrophobic |
| C16 | CB | ARG- 59 | 4.37 | 0 | Hydrophobic |
| O1 | NZ | LYS- 132 | 2.55 | 167.85 | H-Bond (Protein Donor) |
| O1 | NZ | LYS- 132 | 2.55 | 0 | Ionic (Protein Cationic) |
