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
2012-12-07
| Name: | 5-hydroxytryptamine receptor 1B |
|---|---|
| ID: | 5HT1B_HUMAN |
| AC: | P28222 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 86.157 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.409 | 894.375 |
| % Hydrophobic | % Polar |
|---|---|
| 62.64 | 37.36 |
| According to VolSite | |
| HET Code: | 2GM |
|---|---|
| Formula: | C33H38N5O5 |
| Molecular weight: | 584.685 g/mol |
| DrugBank ID: | DB00320 |
| Buried Surface Area: | 67.21 % |
| Polar Surface area: | 119.41 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 8 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -21.0656 | 10.1881 | 21.8573 |
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 |
| C22 | CE2 | TYR- 109 | 4.28 | 0 | Hydrophobic |
| C22 | CZ3 | TRP- 125 | 3.99 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 126 | 3.84 | 0 | Hydrophobic |
| N6 | OD2 | ASP- 129 | 3 | 158.63 | H-Bond (Ligand Donor) |
| N6 | OD2 | ASP- 129 | 3 | 0 | Ionic (Ligand Cationic) |
| N6 | OD1 | ASP- 129 | 3.69 | 0 | Ionic (Ligand Cationic) |
| C15 | CG2 | ILE- 130 | 3.71 | 0 | Hydrophobic |
| C13 | CG1 | ILE- 130 | 3.48 | 0 | Hydrophobic |
| C4 | CB | CYS- 133 | 3.41 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 200 | 4.13 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 201 | 4.35 | 0 | Hydrophobic |
| C32 | CB | VAL- 201 | 3.45 | 0 | Hydrophobic |
| O24 | N | VAL- 201 | 3.01 | 167.4 | H-Bond (Protein Donor) |
| C15 | CB | SER- 212 | 4.3 | 0 | Hydrophobic |
| C16 | CB | ALA- 216 | 4.17 | 0 | Hydrophobic |
| C4 | CH2 | TRP- 327 | 4.23 | 0 | Hydrophobic |
| C10 | CZ | PHE- 330 | 3.61 | 0 | Hydrophobic |
| C30 | CB | SER- 334 | 4.08 | 0 | Hydrophobic |
| C28 | SD | MET- 337 | 4.11 | 0 | Hydrophobic |
| C33 | CE | MET- 337 | 3.82 | 0 | Hydrophobic |
| C38 | CB | LEU- 348 | 3.91 | 0 | Hydrophobic |
| C27 | CZ | PHE- 351 | 3.48 | 0 | Hydrophobic |
| C39 | CB | PHE- 351 | 3.68 | 0 | Hydrophobic |
| C39 | CB | ASP- 352 | 4.47 | 0 | Hydrophobic |
