sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
1999-07-21
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.160 | 6.580 | 6.580 | 2.420 | 9.000 | 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: | 20.259 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.574 | 405.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.50 | 57.50 |
| According to VolSite | |
| HET Code: | BAI |
|---|---|
| Formula: | C16H15N6 |
| Molecular weight: | 291.330 g/mol |
| DrugBank ID: | DB01767 |
| Buried Surface Area: | 55.87 % |
| Polar Surface area: | 108.96 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 14.36 | -12.5892 | 19.5553 |
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' | SG | CYS- 42 | 4.23 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 60 | 3.65 | 143.91 | Pi/Cation |
| C9 | CH2 | TRP- 60 | 4.42 | 0 | Hydrophobic |
| C7 | OD1 | ASP- 195 | 3.69 | 0 | Ionic (Ligand Cationic) |
| C7 | OD2 | ASP- 195 | 3.6 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 195 | 2.83 | 155.63 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 195 | 2.93 | 150.21 | H-Bond (Ligand Donor) |
| C2 | CB | ALA- 196 | 4.14 | 0 | Hydrophobic |
| C4' | CG | GLU- 198 | 4.11 | 0 | Hydrophobic |
| C3 | CB | SER- 201 | 4.46 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 219 | 3.78 | 0 | Hydrophobic |
| N1 | O | GLY- 225 | 2.67 | 125.09 | H-Bond (Ligand Donor) |
| N3 | ZN | ZN- 254 | 2.38 | 0 | Metal Acceptor |
| N4' | ZN | ZN- 254 | 2.43 | 0 | Metal Acceptor |
