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
2013-10-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.660 | 8.660 | 8.660 | 0.000 | 8.660 | 1 |
| Name: | 5-hydroxytryptamine receptor 2B |
|---|---|
| ID: | 5HT2B_HUMAN |
| AC: | P41595 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 75.576 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.445 | 988.875 |
| % Hydrophobic | % Polar |
|---|---|
| 55.63 | 44.37 |
| According to VolSite | |
| HET Code: | ERM |
|---|---|
| Formula: | C33H36N5O5 |
| Molecular weight: | 582.669 g/mol |
| DrugBank ID: | DB00696 |
| Buried Surface Area: | 67.34 % |
| 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 |
|---|---|---|
| -22.0616 | -18.6183 | 12.05 |
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 | CZ3 | TRP- 131 | 4.31 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 132 | 3.83 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 135 | 3.52 | 0 | Ionic (Ligand Cationic) |
| N2 | OD1 | ASP- 135 | 3.01 | 0 | Ionic (Ligand Cationic) |
| N2 | OD1 | ASP- 135 | 3.01 | 154.83 | H-Bond (Ligand Donor) |
| C13 | CG1 | VAL- 136 | 3.88 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 136 | 3.85 | 0 | Hydrophobic |
| C3 | CB | SER- 139 | 3.58 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 208 | 3.91 | 0 | Hydrophobic |
| O3 | N | LEU- 209 | 2.91 | 152.87 | H-Bond (Protein Donor) |
| C29 | CB | LEU- 209 | 3.89 | 0 | Hydrophobic |
| C31 | CB | LYS- 211 | 4.02 | 0 | Hydrophobic |
| C28 | SD | MET- 218 | 4.24 | 0 | Hydrophobic |
| C10 | SD | MET- 218 | 3.53 | 0 | Hydrophobic |
| C30 | CE | MET- 218 | 4.01 | 0 | Hydrophobic |
| C31 | CG | MET- 218 | 3.87 | 0 | Hydrophobic |
| C13 | CB | ALA- 225 | 4.39 | 0 | Hydrophobic |
| C6 | CZ | PHE- 340 | 4.25 | 0 | Hydrophobic |
| C33 | CD2 | LEU- 347 | 3.76 | 0 | Hydrophobic |
| C32 | CG2 | VAL- 348 | 4.19 | 0 | Hydrophobic |
| C22 | CB | GLN- 359 | 4.13 | 0 | Hydrophobic |
| C22 | CB | LEU- 362 | 4.06 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 362 | 4.26 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 362 | 3.99 | 0 | Hydrophobic |
| C22 | CB | GLU- 363 | 3.94 | 0 | Hydrophobic |
