sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
1996-10-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.400 | 5.400 | 5.400 | 0.000 | 5.400 | 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 |
|---|---|
| H | 100 % |
| B-Factor: | 13.248 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.494 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 37.09 | 62.91 |
| According to VolSite | |
| HET Code: | I11 |
|---|---|
| Formula: | C22H36N5O4S |
| Molecular weight: | 466.617 g/mol |
| DrugBank ID: | DB07934 |
| Buried Surface Area: | 56.67 % |
| Polar Surface area: | 130.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -14.0665 | 68.146 | 173.774 |
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 |
| C38 | CB | HIS- 57 | 4.48 | 0 | Hydrophobic |
| C39 | CH2 | TRP- 60 | 4.12 | 0 | Hydrophobic |
| C38 | CZ | TYR- 60 | 3.61 | 0 | Hydrophobic |
| C39 | CE2 | TYR- 60 | 3.67 | 0 | Hydrophobic |
| C6 | CA | ASN- 98 | 4.19 | 0 | Hydrophobic |
| C6 | CG | LEU- 99 | 3.48 | 0 | Hydrophobic |
| C37 | CD1 | LEU- 99 | 3.34 | 0 | Hydrophobic |
| C2 | CG1 | ILE- 174 | 3.81 | 0 | Hydrophobic |
| N31 | OD2 | ASP- 189 | 3.04 | 155.42 | H-Bond (Ligand Donor) |
| N31 | OD1 | ASP- 189 | 3.39 | 145.76 | H-Bond (Ligand Donor) |
| C33 | CB | ALA- 190 | 4.21 | 0 | Hydrophobic |
| C33 | CG1 | VAL- 213 | 3.81 | 0 | Hydrophobic |
| C2 | CE3 | TRP- 215 | 3.77 | 0 | Hydrophobic |
| C4 | CB | TRP- 215 | 4.33 | 0 | Hydrophobic |
| C37 | CB | TRP- 215 | 4.31 | 0 | Hydrophobic |
| C1 | CD2 | TRP- 215 | 4.37 | 0 | Hydrophobic |
| O42 | N | GLY- 216 | 3.1 | 165.67 | H-Bond (Protein Donor) |
| C29 | SG | CYS- 220 | 4.15 | 0 | Hydrophobic |
| O41 | O | HOH- 248 | 2.97 | 146.76 | H-Bond (Protein Donor) |
