sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 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: | 18.578 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.857 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 52.51 | 47.49 |
| According to VolSite | |
| HET Code: | R13 |
|---|---|
| Formula: | C23H29O2 |
| Molecular weight: | 337.475 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.52 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 21.3314 | 27.0152 | 19.0792 |
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 |
| C6 | CD2 | LEU- 19 | 4.44 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 24 | 3.68 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 28 | 4.5 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 28 | 4.12 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 31 | 3.89 | 0 | Hydrophobic |
| C21 | CB | ALA- 32 | 4.05 | 0 | Hydrophobic |
| C9 | CB | ALA- 32 | 3.65 | 0 | Hydrophobic |
| C22 | CB | ALA- 35 | 4.45 | 0 | Hydrophobic |
| C23 | CB | ALA- 36 | 4.36 | 0 | Hydrophobic |
| C23 | CB | PRO- 39 | 3.79 | 0 | Hydrophobic |
| C23 | CG2 | THR- 54 | 3.6 | 0 | Hydrophobic |
| C22 | CG2 | THR- 56 | 4.12 | 0 | Hydrophobic |
| C23 | CG2 | THR- 56 | 3.76 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 58 | 4.04 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 58 | 3.96 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 58 | 4.32 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 58 | 3.53 | 0 | Hydrophobic |
| C20 | CB | ARG- 59 | 4.45 | 0 | Hydrophobic |
| C22 | CB | ARG- 59 | 4.36 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 59 | 3.79 | 18.61 | Pi/Cation |
| C7 | CG1 | VAL- 76 | 4.41 | 0 | Hydrophobic |
| O1 | NE | ARG- 132 | 3.09 | 137.36 | H-Bond (Protein Donor) |
| O1 | NH2 | ARG- 132 | 2.78 | 150.26 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 132 | 3.35 | 0 | Ionic (Protein Cationic) |
| O2 | O | HOH- 207 | 2.65 | 179.98 | H-Bond (Protein Donor) |
