sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2010-11-25
| Name: | Clathrin heavy chain 1 |
|---|---|
| ID: | CLH1_HUMAN |
| AC: | Q00610 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.400 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.601 | 256.500 |
| % Hydrophobic | % Polar |
|---|---|
| 77.63 | 22.37 |
| According to VolSite | |
| HET Code: | VH1 |
|---|---|
| Formula: | C19H13N2O5S |
| Molecular weight: | 381.382 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.44 % |
| Polar Surface area: | 128.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 49.1042 | -9.87652 | 24.135 |
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 |
| CAI | CD1 | ILE- 52 | 3.71 | 0 | Hydrophobic |
| CAX | CD | ARG- 64 | 4.39 | 0 | Hydrophobic |
| CAI | CD | ARG- 64 | 3.63 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 64 | 3.75 | 21.22 | Pi/Cation |
| DuAr | CZ | ARG- 64 | 3.83 | 155.73 | Pi/Cation |
| CAK | CD1 | ILE- 66 | 4.24 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 66 | 3.94 | 0 | Hydrophobic |
| CAK | CG2 | ILE- 80 | 4.2 | 0 | Hydrophobic |
| CAO | CD1 | LEU- 82 | 3.71 | 0 | Hydrophobic |
| OAF | NE2 | GLN- 89 | 2.87 | 134.12 | H-Bond (Protein Donor) |
| DuAr | DuAr | PHE- 91 | 3.74 | 0 | Aromatic Face/Face |
| CAY | CE2 | PHE- 91 | 3.27 | 0 | Hydrophobic |
| CAH | CG2 | ILE- 93 | 3.51 | 0 | Hydrophobic |
| CAR | CG1 | ILE- 93 | 3.57 | 0 | Hydrophobic |
