sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2002-05-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.550 | 7.550 | 7.550 | 0.000 | 7.550 | 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 |
|---|---|
| B | 100 % |
| B-Factor: | 23.826 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.149 | 259.875 |
| % Hydrophobic | % Polar |
|---|---|
| 32.47 | 67.53 |
| According to VolSite | |
| HET Code: | CBB |
|---|---|
| Formula: | C25H33N5O2 |
| Molecular weight: | 435.562 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.34 % |
| Polar Surface area: | 134.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 7.68728 | 6.53113 | 23.2438 |
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 |
| N43 | O | GLU- 97 | 3.39 | 121.16 | H-Bond (Ligand Donor) |
| C33 | CE2 | TYR- 99 | 3.83 | 0 | Hydrophobic |
| C1 | CD | ARG- 143 | 4.17 | 0 | Hydrophobic |
| C1 | CG | GLU- 147 | 4.18 | 0 | Hydrophobic |
| C19 | OD2 | ASP- 189 | 3.42 | 0 | Ionic (Ligand Cationic) |
| C19 | OD1 | ASP- 189 | 3.46 | 0 | Ionic (Ligand Cationic) |
| N20 | OD1 | ASP- 189 | 2.8 | 135.27 | H-Bond (Ligand Donor) |
| N21 | OD2 | ASP- 189 | 2.58 | 144.85 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 190 | 4.26 | 0 | Hydrophobic |
| C5 | CG | GLN- 192 | 3.62 | 0 | Hydrophobic |
| C1 | CB | GLN- 192 | 3.59 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 213 | 3.84 | 0 | Hydrophobic |
| C39 | CE3 | TRP- 215 | 3.36 | 0 | Hydrophobic |
| C34 | CB | TRP- 215 | 3.94 | 0 | Hydrophobic |
| O49 | N | GLY- 216 | 3.34 | 147.09 | H-Bond (Protein Donor) |
| N21 | O | GLY- 219 | 3.06 | 162.41 | H-Bond (Ligand Donor) |
| C11 | SG | CYS- 220 | 4.22 | 0 | Hydrophobic |
| C18 | SG | CYS- 220 | 3.94 | 0 | Hydrophobic |
| C2 | SG | CYS- 220 | 3.57 | 0 | Hydrophobic |
| N44 | O | HOH- 425 | 2.53 | 151.17 | H-Bond (Ligand Donor) |
