sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2009-11-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.090 | 8.090 | 8.090 | 0.000 | 8.090 | 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: | 39.387 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.283 | 283.500 |
| % Hydrophobic | % Polar |
|---|---|
| 34.52 | 65.48 |
| According to VolSite | |
| HET Code: | LGM |
|---|---|
| Formula: | C32H32N7O2 |
| Molecular weight: | 546.642 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.38 % |
| Polar Surface area: | 96.06 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 7 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 36.1364 | 30.9291 | 16.9018 |
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 | 4.1 | 0 | Hydrophobic |
| C26 | CZ | PHE- 174 | 4.16 | 0 | Hydrophobic |
| C1 | CB | PHE- 174 | 3.52 | 0 | Hydrophobic |
| N37 | OD2 | ASP- 189 | 2.93 | 148.06 | H-Bond (Ligand Donor) |
| C31 | CB | GLN- 192 | 4.16 | 0 | Hydrophobic |
| C9 | CB | GLN- 192 | 4.38 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 213 | 3.76 | 0 | Hydrophobic |
| C5 | CE3 | TRP- 215 | 3.48 | 0 | Hydrophobic |
| C4 | CE2 | TRP- 215 | 3.43 | 0 | Hydrophobic |
| C6 | CB | TRP- 215 | 3.82 | 0 | Hydrophobic |
| O40 | N | GLY- 216 | 2.82 | 158.19 | H-Bond (Protein Donor) |
| N36 | O | GLY- 218 | 2.74 | 157.9 | H-Bond (Ligand Donor) |
| C12 | SG | CYS- 220 | 4.03 | 0 | Hydrophobic |
| C31 | SG | CYS- 220 | 4.47 | 0 | Hydrophobic |
| O41 | N | ALA- 221 | 3.28 | 154.56 | H-Bond (Protein Donor) |
| O41 | O | HOH- 436 | 3.04 | 155.52 | H-Bond (Protein Donor) |
