sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.540 Å
X-ray
2009-07-13
| 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: | 16.673 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.205 | 627.750 |
| % Hydrophobic | % Polar |
|---|---|
| 55.91 | 44.09 |
| According to VolSite | |
| HET Code: | DFQ |
|---|---|
| Formula: | C21H17Cl2FN2O2 |
| Molecular weight: | 419.276 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.91 % |
| Polar Surface area: | 51.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -20.8491 | -19.8293 | 3.92232 |
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 |
| CL29 | CG2 | ILE- 1084 | 4.28 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 1084 | 3.41 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 1092 | 4.02 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 1092 | 3.69 | 0 | Hydrophobic |
| CL29 | CG2 | VAL- 1092 | 3.78 | 0 | Hydrophobic |
| C15 | CB | ALA- 1108 | 3.64 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 1140 | 4.08 | 0 | Hydrophobic |
| CL23 | CD2 | LEU- 1140 | 3.77 | 0 | Hydrophobic |
| CL23 | CD1 | LEU- 1157 | 4.39 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 1157 | 3.85 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 1157 | 3.85 | 0 | Hydrophobic |
| N13 | N | MET- 1160 | 2.8 | 158.49 | H-Bond (Protein Donor) |
| C15 | CG | MET- 1160 | 3.95 | 0 | Hydrophobic |
| N2 | O | LYS- 1161 | 2.87 | 150.19 | H-Bond (Ligand Donor) |
| F25 | CB | ASN- 1209 | 4.26 | 0 | Hydrophobic |
| C9 | CE | MET- 1211 | 3.43 | 0 | Hydrophobic |
| C24 | SD | MET- 1211 | 4.18 | 0 | Hydrophobic |
| C10 | CE | MET- 1211 | 3.5 | 0 | Hydrophobic |
| CL23 | CB | ALA- 1221 | 3.64 | 0 | Hydrophobic |
| F25 | CB | ALA- 1221 | 3.24 | 0 | Hydrophobic |
| F25 | CB | ASP- 1222 | 3.6 | 0 | Hydrophobic |
| CL23 | CB | ALA- 1226 | 4.26 | 0 | Hydrophobic |
| C27 | CB | TYR- 1230 | 4.12 | 0 | Hydrophobic |
| CL29 | CD2 | TYR- 1230 | 3.79 | 0 | Hydrophobic |
| C20 | CZ | TYR- 1230 | 3.69 | 0 | Hydrophobic |
