sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2008-04-14
| 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: | 52.949 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.262 | 614.250 |
| % Hydrophobic | % Polar |
|---|---|
| 62.09 | 37.91 |
| According to VolSite | |
| HET Code: | 319 |
|---|---|
| Formula: | C20H16F2N4O3 |
| Molecular weight: | 398.363 g/mol |
| DrugBank ID: | DB06995 |
| Buried Surface Area: | 75.79 % |
| Polar Surface area: | 106.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -0.382172 | 7.23238 | 54.4875 |
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 |
| C16 | CG1 | VAL- 1092 | 4.22 | 0 | Hydrophobic |
| F29 | CG2 | VAL- 1092 | 3.94 | 0 | Hydrophobic |
| F29 | CB | ALA- 1108 | 4.29 | 0 | Hydrophobic |
| C7 | CB | ALA- 1108 | 3.42 | 0 | Hydrophobic |
| O26 | NZ | LYS- 1110 | 3.04 | 159.75 | H-Bond (Protein Donor) |
| F29 | CD | LYS- 1110 | 3.84 | 0 | Hydrophobic |
| N24 | OE2 | GLU- 1127 | 3.02 | 130.13 | H-Bond (Ligand Donor) |
| C20 | CG2 | ILE- 1130 | 4.15 | 0 | Hydrophobic |
| C2 | CE | MET- 1131 | 3.62 | 0 | Hydrophobic |
| C11 | SD | MET- 1131 | 4.13 | 0 | Hydrophobic |
| C20 | CG | MET- 1131 | 3.73 | 0 | Hydrophobic |
| F28 | CE2 | PHE- 1134 | 4.24 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 1139 | 4 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 1140 | 3.75 | 0 | Hydrophobic |
| C8 | CG | LEU- 1157 | 4.24 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 1157 | 3.26 | 0 | Hydrophobic |
| C7 | CG | MET- 1160 | 4.45 | 0 | Hydrophobic |
| N21 | N | MET- 1160 | 2.8 | 147.92 | H-Bond (Protein Donor) |
| N22 | O | MET- 1160 | 2.96 | 129.96 | H-Bond (Ligand Donor) |
| F28 | CD1 | LEU- 1195 | 3.4 | 0 | Hydrophobic |
| F28 | CE2 | PHE- 1200 | 3.8 | 0 | Hydrophobic |
| C4 | SD | MET- 1211 | 3.99 | 0 | Hydrophobic |
| C9 | CE | MET- 1211 | 3.67 | 0 | Hydrophobic |
| F28 | CG1 | VAL- 1220 | 4.2 | 0 | Hydrophobic |
| C2 | CB | ALA- 1221 | 4.46 | 0 | Hydrophobic |
| C3 | CB | ALA- 1221 | 4.37 | 0 | Hydrophobic |
| N23 | O | ASP- 1222 | 3.01 | 122.74 | H-Bond (Ligand Donor) |
| O25 | N | ASP- 1222 | 2.74 | 154.8 | H-Bond (Protein Donor) |
| C1 | CB | ASP- 1222 | 3.35 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 1223 | 2.99 | 0 | Hydrophobic |
