sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2009-11-12
| Name: | Protein S100-A4 |
|---|---|
| ID: | S10A4_HUMAN |
| AC: | P26447 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| G | 35 % |
| H | 46 % |
| I | 8 % |
| J | 12 % |
| B-Factor: | 24.874 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.050 | 2737.125 |
| % Hydrophobic | % Polar |
|---|---|
| 49.45 | 50.55 |
| According to VolSite | |
| HET Code: | TFP |
|---|---|
| Formula: | C21H25F3N3S |
| Molecular weight: | 408.503 g/mol |
| DrugBank ID: | DB00831 |
| Buried Surface Area: | 50.47 % |
| Polar Surface area: | 36.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 41.4461 | 44.6829 | 40.9109 |
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 |
| C2 | CG | GLU- 6 | 4.04 | 0 | Hydrophobic |
| C3 | CB | GLU- 6 | 4.23 | 0 | Hydrophobic |
| F2 | CG | GLU- 6 | 3.66 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 9 | 4.04 | 0 | Hydrophobic |
| C3 | CB | LEU- 9 | 4.01 | 0 | Hydrophobic |
| S | CB | ASP- 10 | 3.62 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 10 | 2.79 | 175.78 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 10 | 3.27 | 121.17 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 10 | 2.79 | 0 | Ionic (Ligand Cationic) |
| N3 | OD2 | ASP- 10 | 3.27 | 0 | Ionic (Ligand Cationic) |
| F2 | CD2 | LEU- 42 | 3.93 | 0 | Hydrophobic |
| F1 | CB | SER- 44 | 3.29 | 0 | Hydrophobic |
| F1 | CB | PHE- 45 | 3.82 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 82 | 3.98 | 0 | Hydrophobic |
| F3 | CG2 | ILE- 82 | 3.6 | 0 | Hydrophobic |
| C9 | CB | CYS- 86 | 3.8 | 0 | Hydrophobic |
| C4 | SG | CYS- 86 | 3.7 | 0 | Hydrophobic |
| C7 | SG | CYS- 86 | 3.57 | 0 | Hydrophobic |
| C13 | CZ | PHE- 89 | 3.83 | 0 | Hydrophobic |
| C14 | CE2 | PHE- 89 | 3.6 | 0 | Hydrophobic |
| C10 | CB | PHE- 89 | 3.73 | 0 | Hydrophobic |
| F1 | CZ | PHE- 89 | 3.22 | 0 | Hydrophobic |
