sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2001-10-09
| Name: | Protein S100-A9 |
|---|---|
| ID: | S10A9_HUMAN |
| AC: | P06702 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 17 % |
| E | 83 % |
| B-Factor: | 48.445 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.731 | 418.500 |
| % Hydrophobic | % Polar |
|---|---|
| 53.23 | 46.77 |
| According to VolSite | |
| HET Code: | CPS |
|---|---|
| Formula: | C32H58N2O7S |
| Molecular weight: | 614.877 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 44.73 % |
| Polar Surface area: | 155.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 10.614 | 16.6627 | 33.0984 |
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 |
| C8 | CD2 | LEU- 49 | 4.07 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 49 | 4.48 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 49 | 4.17 | 0 | Hydrophobic |
| C13 | CG | LYS- 51 | 4.38 | 0 | Hydrophobic |
| C10 | CG | GLU- 52 | 3.36 | 0 | Hydrophobic |
| C13 | CG | GLU- 52 | 4.17 | 0 | Hydrophobic |
| O2 | OE1 | GLU- 52 | 2.73 | 164.92 | H-Bond (Ligand Donor) |
| C10 | CG1 | VAL- 58 | 4.4 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 58 | 3.66 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 58 | 4.5 | 0 | Hydrophobic |
| C11 | CB | HIS- 61 | 3.63 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 62 | 3.81 | 0 | Hydrophobic |
| C17 | CG1 | ILE- 62 | 3.91 | 0 | Hydrophobic |
| C18 | CG1 | ILE- 62 | 3.83 | 0 | Hydrophobic |
| C16 | CB | ASP- 65 | 4.15 | 0 | Hydrophobic |
| C7 | CD | ARG- 85 | 4.3 | 0 | Hydrophobic |
| C8 | CB | ARG- 85 | 4.26 | 0 | Hydrophobic |
