sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-01-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.500 | 8.500 | 8.500 | 0.000 | 8.500 | 1 |
| Name: | Hepatocyte growth factor receptor |
|---|---|
| ID: | MET_HUMAN |
| AC: | P08581 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.436 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.118 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 56.59 | 43.41 |
| According to VolSite | |
| HET Code: | 0JJ |
|---|---|
| Formula: | C19H17N8OS |
| Molecular weight: | 405.456 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.87 % |
| Polar Surface area: | 132.5 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 20.1105 | 11.2827 | 57.9129 |
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 |
| C17 | CD1 | ILE- 1084 | 3.7 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 1092 | 4.25 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 1092 | 4.06 | 0 | Hydrophobic |
| C12 | CB | ALA- 1108 | 3.73 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 1157 | 3.77 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 1157 | 3.98 | 0 | Hydrophobic |
| C19 | CE2 | TYR- 1159 | 4.09 | 0 | Hydrophobic |
| N7 | N | MET- 1160 | 3.08 | 151.83 | H-Bond (Protein Donor) |
| C16 | CB | MET- 1160 | 4.3 | 0 | Hydrophobic |
| C7 | CB | ASP- 1164 | 4.39 | 0 | Hydrophobic |
| C11 | CE | MET- 1211 | 3.8 | 0 | Hydrophobic |
| C12 | SD | MET- 1211 | 3.84 | 0 | Hydrophobic |
| C16 | CE | MET- 1211 | 3.78 | 0 | Hydrophobic |
| N4 | N | ASP- 1222 | 3.09 | 145.27 | H-Bond (Protein Donor) |
| C7 | CB | TYR- 1230 | 4.36 | 0 | Hydrophobic |
| C10 | CZ | TYR- 1230 | 3.97 | 0 | Hydrophobic |
