sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.840 Å
X-ray
2010-07-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.050 | 8.050 | 8.050 | 0.000 | 8.050 | 1 |
| Name: | Beta-2 adrenergic receptor |
|---|---|
| ID: | ADRB2_HUMAN |
| AC: | P07550 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.195 | 995.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.25 | 44.75 |
| According to VolSite | |
| HET Code: | JSZ |
|---|---|
| Formula: | C18H26NO5 |
| Molecular weight: | 336.403 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.74 % |
| Polar Surface area: | 85.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 2.15833 | 3.80988 | 51.8125 |
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 |
| C17 | CH2 | TRP- 109 | 3.78 | 0 | Hydrophobic |
| C18 | CG2 | THR- 110 | 3.77 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 113 | 3.76 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 113 | 2.83 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 113 | 2.83 | 135.68 | H-Bond (Ligand Donor) |
| O5 | OD1 | ASP- 113 | 2.66 | 164 | H-Bond (Ligand Donor) |
| O5 | OD2 | ASP- 113 | 3.13 | 132.88 | H-Bond (Ligand Donor) |
| C12 | CG2 | VAL- 114 | 3.71 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 114 | 3.7 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 117 | 4.26 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 117 | 3.67 | 0 | Hydrophobic |
| C2 | CE2 | PHE- 193 | 4.37 | 0 | Hydrophobic |
| C3 | CD2 | PHE- 193 | 3.95 | 0 | Hydrophobic |
| C6 | CE2 | PHE- 193 | 3.45 | 0 | Hydrophobic |
| C18 | CD2 | PHE- 193 | 3.69 | 0 | Hydrophobic |
| C3 | CG2 | THR- 195 | 4.03 | 0 | Hydrophobic |
| C2 | CB | ALA- 200 | 4.02 | 0 | Hydrophobic |
| C9 | CB | SER- 207 | 3.55 | 0 | Hydrophobic |
| C13 | CZ3 | TRP- 286 | 3.88 | 0 | Hydrophobic |
| C6 | CZ | PHE- 289 | 3.99 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 289 | 3.69 | 0 | Hydrophobic |
| C14 | CZ | PHE- 289 | 3.99 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 293 | 2.69 | 160.12 | H-Bond (Protein Donor) |
| C3 | CZ | TYR- 308 | 4.36 | 0 | Hydrophobic |
| N1 | OD1 | ASN- 312 | 3.05 | 139.15 | H-Bond (Ligand Donor) |
| O5 | ND2 | ASN- 312 | 2.99 | 160.95 | H-Bond (Protein Donor) |
