sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
1994-09-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.400 | 9.400 | 9.400 | 0.000 | 9.400 | 2 |
| Name: | Cellular retinoic acid-binding protein 1 |
|---|---|
| ID: | RABP1_MOUSE |
| AC: | P62965 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 91 % |
| B | 9 % |
| B-Factor: | 34.548 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.393 | 1056.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.59 | 44.41 |
| According to VolSite | |
| HET Code: | REA |
|---|---|
| Formula: | C20H27O2 |
| Molecular weight: | 299.427 g/mol |
| DrugBank ID: | DB00755 |
| Buried Surface Area: | 62.88 % |
| 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 |
|---|---|---|
| 4.63486 | 6.64127 | -8.21082 |
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 | 4.01 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 24 | 4.41 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 24 | 4.4 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 28 | 3.93 | 0 | Hydrophobic |
| C17 | CB | VAL- 31 | 4.26 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 31 | 4.22 | 0 | Hydrophobic |
| C17 | CB | ALA- 32 | 4.3 | 0 | Hydrophobic |
| C18 | CB | ALA- 32 | 4.28 | 0 | Hydrophobic |
| C19 | CB | ALA- 36 | 3.98 | 0 | Hydrophobic |
| C20 | CB | ALA- 36 | 4.38 | 0 | Hydrophobic |
| C20 | CB | PRO- 39 | 3.6 | 0 | Hydrophobic |
| C20 | CG2 | THR- 54 | 3.81 | 0 | Hydrophobic |
| C20 | CG2 | THR- 56 | 3.48 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 58 | 4.21 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 58 | 3.96 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 58 | 4.11 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 58 | 4.13 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 58 | 3.94 | 0 | Hydrophobic |
| C16 | CB | ARG- 59 | 4.14 | 0 | Hydrophobic |
| C18 | CB | ASP- 77 | 4.22 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 131 | 3.27 | 141.12 | H-Bond (Protein Donor) |
| O1 | NE | ARG- 131 | 3 | 158.08 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 131 | 3.58 | 0 | Ionic (Protein Cationic) |
| O2 | OH | TYR- 133 | 3.31 | 120.59 | H-Bond (Protein Donor) |
| O2 | O | HOH- 201 | 3.32 | 140.85 | H-Bond (Protein Donor) |
