sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2002-04-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.080 | 9.080 | 9.080 | 0.000 | 9.080 | 1 |
| Name: | Sex hormone-binding globulin |
|---|---|
| ID: | SHBG_HUMAN |
| AC: | P04278 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 29.116 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.650 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 70.00 | 30.00 |
| According to VolSite | |
| HET Code: | ESM |
|---|---|
| Formula: | C19H26O3 |
| Molecular weight: | 302.408 g/mol |
| DrugBank ID: | DB02342 |
| Buried Surface Area: | 73.57 % |
| Polar Surface area: | 49.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 21.9678 | 10.9303 | 32.7832 |
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 |
| O17 | OG | SER- 42 | 2.86 | 164.45 | H-Bond (Protein Donor) |
| C16 | CB | SER- 42 | 4.09 | 0 | Hydrophobic |
| C17 | CZ | PHE- 56 | 4.04 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 56 | 3.83 | 0 | Hydrophobic |
| C9 | CG | PHE- 67 | 3.83 | 0 | Hydrophobic |
| C10 | CB | PHE- 67 | 3.8 | 0 | Hydrophobic |
| C6 | CB | PHE- 67 | 3.58 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 80 | 4.1 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 80 | 3.63 | 0 | Hydrophobic |
| O3 | ND2 | ASN- 82 | 3.09 | 166.48 | H-Bond (Protein Donor) |
| O2 | ND2 | ASN- 82 | 3.01 | 122.5 | H-Bond (Protein Donor) |
| C12 | CG1 | VAL- 105 | 3.9 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 105 | 4.26 | 0 | Hydrophobic |
| O17 | O | VAL- 105 | 3.09 | 153.67 | H-Bond (Ligand Donor) |
| C1 | SD | MET- 107 | 4.41 | 0 | Hydrophobic |
| C11 | SD | MET- 107 | 4 | 0 | Hydrophobic |
| C19 | SD | MET- 107 | 3.92 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 112 | 4.42 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 112 | 3.54 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 127 | 3.7 | 0 | Hydrophobic |
| C19 | CB | SER- 128 | 4.38 | 0 | Hydrophobic |
| O3 | NZ | LYS- 134 | 2.85 | 143.34 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 134 | 2.69 | 132.15 | H-Bond (Protein Donor) |
| C3 | CD | LYS- 134 | 3.85 | 0 | Hydrophobic |
| C15 | SD | MET- 139 | 4.11 | 0 | Hydrophobic |
| C18 | SD | MET- 139 | 4.34 | 0 | Hydrophobic |
| C6 | CE | MET- 139 | 4.09 | 0 | Hydrophobic |
| C8 | SD | MET- 139 | 4.05 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 141 | 3.54 | 0 | Hydrophobic |
| C16 | CE3 | TRP- 170 | 4.47 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 171 | 3.9 | 0 | Hydrophobic |
