sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2002-05-10
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.050 | 8.050 | 8.050 | 0.000 | 8.050 | 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: | 23.552 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.172 | 290.250 |
| % Hydrophobic | % Polar |
|---|---|
| 32.56 | 67.44 |
| According to VolSite | |
| HET Code: | CMI |
|---|---|
| Formula: | C27H29N4O |
| Molecular weight: | 425.545 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.2 % |
| Polar Surface area: | 85.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 7.56669 | 6.98875 | 23.2328 |
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 | CD | ARG- 143 | 4.12 | 0 | Hydrophobic |
| C1 | CG | GLU- 147 | 4.23 | 0 | Hydrophobic |
| C37 | CE2 | PHE- 174 | 3.56 | 0 | Hydrophobic |
| C31 | OD2 | ASP- 189 | 3.72 | 0 | Ionic (Ligand Cationic) |
| C31 | OD1 | ASP- 189 | 3.56 | 0 | Ionic (Ligand Cationic) |
| N32 | OD1 | ASP- 189 | 3.37 | 127.5 | H-Bond (Ligand Donor) |
| N53 | OD1 | ASP- 189 | 2.92 | 140.57 | H-Bond (Ligand Donor) |
| C23 | CB | ALA- 190 | 4.26 | 0 | Hydrophobic |
| C21 | CG | GLN- 192 | 4.5 | 0 | Hydrophobic |
| C1 | CB | GLN- 192 | 3.69 | 0 | Hydrophobic |
| C5 | CG | GLN- 192 | 3.21 | 0 | Hydrophobic |
| C22 | CB | SER- 195 | 4.42 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 213 | 3.58 | 0 | Hydrophobic |
| C33 | CD2 | TRP- 215 | 3.77 | 0 | Hydrophobic |
| C37 | CE3 | TRP- 215 | 4.03 | 0 | Hydrophobic |
| C28 | CE3 | TRP- 215 | 3.19 | 0 | Hydrophobic |
| C14 | CB | TRP- 215 | 3.77 | 0 | Hydrophobic |
| C37 | CG | GLU- 217 | 3.72 | 0 | Hydrophobic |
| C3 | SG | CYS- 220 | 4.32 | 0 | Hydrophobic |
| C2 | SG | CYS- 220 | 3.67 | 0 | Hydrophobic |
| C25 | SG | CYS- 220 | 3.99 | 0 | Hydrophobic |
