sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2012-11-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.990 | 7.990 | 7.990 | 0.000 | 7.990 | 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: | 26.250 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.188 | 367.875 |
| % Hydrophobic | % Polar |
|---|---|
| 59.63 | 40.37 |
| According to VolSite | |
| HET Code: | W9Z |
|---|---|
| Formula: | C20H17N7 |
| Molecular weight: | 355.396 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.31 % |
| Polar Surface area: | 73.78 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 20.103 | 84.1119 | 4.95952 |
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 | 4.45 | 0 | Hydrophobic |
| C18 | CG1 | ILE- 1084 | 3.7 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 1084 | 3.69 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 1092 | 4.02 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 1092 | 3.63 | 0 | Hydrophobic |
| C17 | CB | ALA- 1108 | 4.28 | 0 | Hydrophobic |
| C2 | CB | ALA- 1108 | 3.47 | 0 | Hydrophobic |
| C15 | CB | LYS- 1110 | 4.19 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 1157 | 3.43 | 0 | Hydrophobic |
| N1 | N | MET- 1160 | 2.99 | 159.79 | H-Bond (Protein Donor) |
| C2 | CG | MET- 1160 | 3.91 | 0 | Hydrophobic |
| C17 | CE | MET- 1211 | 3.6 | 0 | Hydrophobic |
| C17 | CE | MET- 1211 | 3.6 | 0 | Hydrophobic |
| N6 | N | ASP- 1222 | 2.95 | 145.37 | H-Bond (Protein Donor) |
| C15 | CB | ALA- 1226 | 4.3 | 0 | Hydrophobic |
| C5 | CZ | TYR- 1230 | 3.86 | 0 | Hydrophobic |
| N4 | O | HOH- 2083 | 2.87 | 159.56 | H-Bond (Protein Donor) |
