sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2008-02-28
| 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: | 69.243 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.035 | 1670.625 |
| % Hydrophobic | % Polar |
|---|---|
| 62.63 | 37.37 |
| According to VolSite | |
| HET Code: | 1FN |
|---|---|
| Formula: | C25H16F2N4O3 |
| Molecular weight: | 458.416 g/mol |
| DrugBank ID: | DB06896 |
| Buried Surface Area: | 66.1 % |
| Polar Surface area: | 87.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 21.035 | 17.0953 | 57.2289 |
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 |
| C1 | CD1 | ILE- 1084 | 4.04 | 0 | Hydrophobic |
| F14 | CG1 | VAL- 1092 | 3.44 | 0 | Hydrophobic |
| F14 | CB | ALA- 1108 | 4.37 | 0 | Hydrophobic |
| C5 | CB | ALA- 1108 | 3.33 | 0 | Hydrophobic |
| F14 | CG | LYS- 1110 | 3.5 | 0 | Hydrophobic |
| C12 | CD | LYS- 1110 | 4.23 | 0 | Hydrophobic |
| C31 | CE | MET- 1131 | 4.15 | 0 | Hydrophobic |
| C30 | CE | MET- 1131 | 3.76 | 0 | Hydrophobic |
| F35 | CE2 | PHE- 1134 | 4.14 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 1139 | 3.95 | 0 | Hydrophobic |
| F35 | CG1 | VAL- 1139 | 4.08 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 1140 | 3.92 | 0 | Hydrophobic |
| C12 | CG | LEU- 1157 | 4.44 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 1157 | 3.67 | 0 | Hydrophobic |
| N3 | N | MET- 1160 | 3.14 | 159.18 | H-Bond (Protein Donor) |
| C5 | CG | MET- 1160 | 4.48 | 0 | Hydrophobic |
| N29 | O | MET- 1160 | 3.38 | 139.24 | H-Bond (Ligand Donor) |
| F35 | CD1 | LEU- 1195 | 3.66 | 0 | Hydrophobic |
| F35 | CE2 | PHE- 1200 | 4.32 | 0 | Hydrophobic |
| C1 | CE | MET- 1211 | 3.27 | 0 | Hydrophobic |
| C5 | CE | MET- 1211 | 3.59 | 0 | Hydrophobic |
| C9 | CE | MET- 1211 | 3.5 | 0 | Hydrophobic |
| F35 | CG1 | VAL- 1220 | 3.63 | 0 | Hydrophobic |
| C10 | CB | ALA- 1221 | 4.21 | 0 | Hydrophobic |
| C30 | CB | ALA- 1221 | 4.39 | 0 | Hydrophobic |
| O25 | N | ASP- 1222 | 2.86 | 154.39 | H-Bond (Protein Donor) |
| C34 | CB | ASP- 1222 | 3.38 | 0 | Hydrophobic |
