sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2009-11-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.300 | 9.300 | 9.300 | 0.000 | 9.300 | 1 |
| Name: | Coagulation factor X |
|---|---|
| ID: | FA10_HUMAN |
| AC: | P00742 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.21.6 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 35.054 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.171 | 243.000 |
| % Hydrophobic | % Polar |
|---|---|
| 34.72 | 65.28 |
| According to VolSite | |
| HET Code: | LGJ |
|---|---|
| Formula: | C26H18F4N6O4S |
| Molecular weight: | 586.518 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.25 % |
| Polar Surface area: | 142.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 36.02 | 30.7599 | 16.3644 |
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 |
| C1 | CB | TYR- 99 | 3.83 | 0 | Hydrophobic |
| F39 | CD | ARG- 143 | 4.47 | 0 | Hydrophobic |
| F38 | CG | GLU- 146 | 3.49 | 0 | Hydrophobic |
| F39 | CG | GLU- 146 | 4.48 | 0 | Hydrophobic |
| C25 | CE1 | PHE- 174 | 3.93 | 0 | Hydrophobic |
| F37 | CE2 | PHE- 174 | 4.11 | 0 | Hydrophobic |
| C9 | CD1 | PHE- 174 | 3.47 | 0 | Hydrophobic |
| C1 | CB | PHE- 174 | 3.72 | 0 | Hydrophobic |
| N31 | OD2 | ASP- 189 | 2.74 | 144.03 | H-Bond (Ligand Donor) |
| F39 | SG | CYS- 191 | 3.83 | 0 | Hydrophobic |
| C7 | CB | GLN- 192 | 4.47 | 0 | Hydrophobic |
| F39 | CB | GLN- 192 | 3.53 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 213 | 3.8 | 0 | Hydrophobic |
| F37 | CE3 | TRP- 215 | 4.21 | 0 | Hydrophobic |
| C8 | CB | TRP- 215 | 3.75 | 0 | Hydrophobic |
| O34 | N | GLY- 216 | 3.46 | 156.98 | H-Bond (Protein Donor) |
| F37 | CG | GLU- 217 | 3.71 | 0 | Hydrophobic |
| N30 | O | GLY- 218 | 2.81 | 163.37 | H-Bond (Ligand Donor) |
| C11 | SG | CYS- 220 | 3.91 | 0 | Hydrophobic |
| F39 | SG | CYS- 220 | 3.88 | 0 | Hydrophobic |
| O33 | N | ALA- 221 | 3.13 | 152.36 | H-Bond (Protein Donor) |
| O33 | O | HOH- 424 | 2.88 | 151.67 | H-Bond (Protein Donor) |
