sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-06-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.520 | 9.540 | 9.540 | 0.020 | 9.570 | 2 |
| Name: | Prothrombin |
|---|---|
| ID: | THRB_HUMAN |
| AC: | P00734 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.21.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| H | 100 % |
| B-Factor: | 19.190 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.827 | 901.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.82 | 59.18 |
| According to VolSite | |
| HET Code: | N5N |
|---|---|
| Formula: | C26H34N6O6S |
| Molecular weight: | 558.650 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59 % |
| Polar Surface area: | 198.93 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 16.655 | -13.5911 | 22.7003 |
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 |
| O12 | NE2 | HIS- 57 | 2.57 | 137.72 | H-Bond (Protein Donor) |
| C5 | CE2 | TYR- 60 | 3.87 | 0 | Hydrophobic |
| C6 | CZ | TYR- 60 | 4.05 | 0 | Hydrophobic |
| C5 | CH2 | TRP- 60 | 4.02 | 0 | Hydrophobic |
| C6 | CZ2 | TRP- 60 | 4.08 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 99 | 4.46 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 99 | 4.33 | 0 | Hydrophobic |
| C35 | CG | LEU- 99 | 3.7 | 0 | Hydrophobic |
| C25 | CG1 | ILE- 174 | 4.29 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 174 | 4.14 | 0 | Hydrophobic |
| C37 | OD1 | ASP- 189 | 3.53 | 0 | Ionic (Ligand Cationic) |
| C37 | OD2 | ASP- 189 | 3.77 | 0 | Ionic (Ligand Cationic) |
| N38 | OD1 | ASP- 189 | 3.47 | 127.03 | H-Bond (Ligand Donor) |
| N38 | OD2 | ASP- 189 | 2.85 | 177.37 | H-Bond (Ligand Donor) |
| N39 | OD1 | ASP- 189 | 2.84 | 162.68 | H-Bond (Ligand Donor) |
| C36 | CG1 | VAL- 213 | 3.92 | 0 | Hydrophobic |
| C25 | CE3 | TRP- 215 | 3.34 | 0 | Hydrophobic |
| C25 | CB | TRP- 215 | 3.9 | 0 | Hydrophobic |
| O8 | N | GLY- 216 | 3.09 | 158.07 | H-Bond (Protein Donor) |
| O20 | N | GLY- 219 | 3.27 | 142.22 | H-Bond (Protein Donor) |
| N38 | O | GLY- 219 | 2.75 | 146.25 | H-Bond (Ligand Donor) |
| C26 | SG | CYS- 220 | 4.03 | 0 | Hydrophobic |
