sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.810 Å
X-ray
2004-03-05
| 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: | 18.322 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.098 | 276.750 |
| % Hydrophobic | % Polar |
|---|---|
| 37.80 | 62.20 |
| According to VolSite | |
| HET Code: | 170 |
|---|---|
| Formula: | C21H17Cl2F2N9O3 |
| Molecular weight: | 552.321 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.25 % |
| Polar Surface area: | 142.85 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 16.5921 | -14.0093 | 22.8074 |
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 |
| CL2 | CB | HIS- 57 | 4.15 | 0 | Hydrophobic |
| CL2 | CH2 | TRP- 60 | 3.58 | 0 | Hydrophobic |
| C33 | CH2 | TRP- 60 | 4.48 | 0 | Hydrophobic |
| CL2 | CZ | TYR- 60 | 3.61 | 0 | Hydrophobic |
| CL2 | CD1 | LEU- 99 | 3.84 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 99 | 4.02 | 0 | Hydrophobic |
| C6 | CG | LEU- 99 | 3.89 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 174 | 4.11 | 0 | Hydrophobic |
| F2 | CG1 | ILE- 174 | 3.93 | 0 | Hydrophobic |
| F1 | CD1 | ILE- 174 | 3.5 | 0 | Hydrophobic |
| CL1 | CB | ALA- 190 | 4.03 | 0 | Hydrophobic |
| C44 | CB | ALA- 190 | 3.96 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 213 | 3.56 | 0 | Hydrophobic |
| C43 | CG1 | VAL- 213 | 3.51 | 0 | Hydrophobic |
| N37 | O | SER- 214 | 2.93 | 155.8 | H-Bond (Ligand Donor) |
| C33 | CB | TRP- 215 | 4.06 | 0 | Hydrophobic |
| C8 | CE3 | TRP- 215 | 3.47 | 0 | Hydrophobic |
| C8 | CB | TRP- 215 | 4.15 | 0 | Hydrophobic |
| F2 | CE3 | TRP- 215 | 3.24 | 0 | Hydrophobic |
| N18 | O | GLY- 216 | 2.85 | 175.93 | H-Bond (Ligand Donor) |
| O28 | N | GLY- 216 | 2.98 | 163.64 | H-Bond (Protein Donor) |
| F2 | CB | GLU- 217 | 4.22 | 0 | Hydrophobic |
| C11 | CG | GLU- 217 | 3.94 | 0 | Hydrophobic |
| C47 | SG | CYS- 220 | 4.29 | 0 | Hydrophobic |
| CL1 | CZ | TYR- 228 | 4.05 | 0 | Hydrophobic |
