sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2012-12-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.510 | 8.570 | 8.520 | 0.080 | 8.680 | 3 |
| 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: | 80.112 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.482 | 968.625 |
| % Hydrophobic | % Polar |
|---|---|
| 60.98 | 39.02 |
| According to VolSite | |
| HET Code: | ERM |
|---|---|
| Formula: | C33H36N5O5 |
| Molecular weight: | 582.669 g/mol |
| DrugBank ID: | DB00696 |
| Buried Surface Area: | 66.73 % |
| 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 |
|---|---|---|
| -12.0073 | -17.6083 | 20.8551 |
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 |
| C26 | CE2 | TYR- 109 | 4.44 | 0 | Hydrophobic |
| C26 | CZ3 | TRP- 125 | 3.92 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 126 | 3.72 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 129 | 3.79 | 0 | Ionic (Ligand Cationic) |
| N2 | OD2 | ASP- 129 | 2.72 | 0 | Ionic (Ligand Cationic) |
| N2 | OD2 | ASP- 129 | 2.72 | 171.43 | H-Bond (Ligand Donor) |
| C13 | CG2 | ILE- 130 | 3.87 | 0 | Hydrophobic |
| C9 | CG1 | ILE- 130 | 4.18 | 0 | Hydrophobic |
| C3 | CB | CYS- 133 | 3.35 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 200 | 4.16 | 0 | Hydrophobic |
| O3 | N | VAL- 201 | 3.21 | 160.88 | H-Bond (Protein Donor) |
| C32 | CG2 | VAL- 201 | 3.25 | 0 | Hydrophobic |
| C12 | CB | SER- 212 | 4.27 | 0 | Hydrophobic |
| C13 | CB | ALA- 216 | 4.12 | 0 | Hydrophobic |
| C3 | CH2 | TRP- 327 | 4.26 | 0 | Hydrophobic |
| C6 | CZ | PHE- 330 | 3.91 | 0 | Hydrophobic |
| C30 | CB | SER- 334 | 4.24 | 0 | Hydrophobic |
| C28 | SD | MET- 337 | 4.18 | 0 | Hydrophobic |
| C33 | CE | MET- 337 | 3.76 | 0 | Hydrophobic |
| C22 | CG | LEU- 348 | 4.01 | 0 | Hydrophobic |
| C27 | CZ | PHE- 351 | 3.48 | 0 | Hydrophobic |
| C22 | CB | PHE- 351 | 3.6 | 0 | Hydrophobic |
