sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2004-10-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.520 | 8.520 | 8.520 | 0.000 | 8.520 | 1 |
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 27.733 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.489 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 38.36 | 61.64 |
| According to VolSite | |
| HET Code: | GAH |
|---|---|
| Formula: | C38H63N11O6 |
| Molecular weight: | 769.977 g/mol |
| DrugBank ID: | DB04697 |
| Buried Surface Area: | 50.26 % |
| Polar Surface area: | 298.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 11 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 21 |
| X | Y | Z |
|---|---|---|
| 12.837 | -14.7946 | 14.0839 |
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 |
| C27 | CB | HIS- 57 | 4.34 | 0 | Hydrophobic |
| C27 | CZ | TYR- 60 | 4.35 | 0 | Hydrophobic |
| C27 | CH2 | TRP- 60 | 4 | 0 | Hydrophobic |
| C51 | CH2 | TRP- 60 | 3.64 | 0 | Hydrophobic |
| C20 | CB | ASN- 98 | 4.37 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 99 | 4.32 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 99 | 3.62 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 99 | 4.23 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 174 | 4.48 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 174 | 4.12 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 174 | 3.55 | 0 | Hydrophobic |
| O40 | OD1 | ASP- 189 | 3.36 | 171.32 | H-Bond (Ligand Donor) |
| C38 | CB | ALA- 190 | 3.65 | 0 | Hydrophobic |
| C49 | CG | GLU- 192 | 4.47 | 0 | Hydrophobic |
| C33 | CB | SER- 195 | 3.38 | 0 | Hydrophobic |
| C34 | CG1 | VAL- 213 | 3.77 | 0 | Hydrophobic |
| C35 | CG1 | VAL- 213 | 3.3 | 0 | Hydrophobic |
| N31 | O | SER- 214 | 3.36 | 143.84 | H-Bond (Ligand Donor) |
| C19 | CD2 | TRP- 215 | 3.62 | 0 | Hydrophobic |
| C16 | CE3 | TRP- 215 | 3.62 | 0 | Hydrophobic |
| O24 | N | GLY- 216 | 3.39 | 172.79 | H-Bond (Protein Donor) |
| C1 | CB | GLU- 217 | 3.85 | 0 | Hydrophobic |
| O46 | N | GLY- 219 | 2.76 | 157.08 | H-Bond (Protein Donor) |
| N47 | O | GLY- 219 | 2.95 | 126.73 | H-Bond (Ligand Donor) |
