sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1999-02-22
| 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: | 21.063 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.399 | 678.375 |
| % Hydrophobic | % Polar |
|---|---|
| 56.72 | 43.28 |
| According to VolSite | |
| HET Code: | R12 |
|---|---|
| Formula: | C20H23O3 |
| Molecular weight: | 311.395 g/mol |
| DrugBank ID: | DB08455 |
| Buried Surface Area: | 59.82 % |
| Polar Surface area: | 60.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 18.727 | -3.19982 | 20.0149 |
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 |
| C23 | CD2 | LEU- 19 | 3.93 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 24 | 4.1 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 24 | 4.09 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 28 | 3.57 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 28 | 4.05 | 0 | Hydrophobic |
| C19 | CB | ALA- 32 | 4.3 | 0 | Hydrophobic |
| C23 | CB | ALA- 32 | 3.93 | 0 | Hydrophobic |
| C19 | CB | ALA- 35 | 4.04 | 0 | Hydrophobic |
| C18 | CB | ALA- 36 | 3.83 | 0 | Hydrophobic |
| C18 | CB | PRO- 39 | 3.72 | 0 | Hydrophobic |
| C18 | CG2 | THR- 54 | 3.7 | 0 | Hydrophobic |
| C18 | CG2 | THR- 56 | 3.7 | 0 | Hydrophobic |
| C19 | CG2 | THR- 56 | 4.45 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 58 | 3.67 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 58 | 4.04 | 0 | Hydrophobic |
| C19 | CB | ARG- 59 | 4.26 | 0 | Hydrophobic |
| C20 | CB | ARG- 59 | 3.96 | 0 | Hydrophobic |
| C4 | CD | ARG- 59 | 4.36 | 0 | Hydrophobic |
| C2 | CB | ASP- 77 | 4.4 | 0 | Hydrophobic |
| O3 | NH2 | ARG- 132 | 2.7 | 145.52 | H-Bond (Protein Donor) |
| O3 | NE | ARG- 132 | 2.89 | 137.73 | H-Bond (Protein Donor) |
| O3 | CZ | ARG- 132 | 3.21 | 0 | Ionic (Protein Cationic) |
| O2 | O | HOH- 334 | 2.66 | 179.94 | H-Bond (Protein Donor) |
