sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.270 Å
X-ray
2012-08-06
| 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: | 24.703 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.427 | 523.125 |
| % Hydrophobic | % Polar |
|---|---|
| 60.65 | 39.35 |
| According to VolSite | |
| HET Code: | 0J8 |
|---|---|
| Formula: | C23H22F3N8O2 |
| Molecular weight: | 499.468 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.67 % |
| Polar Surface area: | 130.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -3.33031 | -16.8928 | 14.7384 |
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 |
| CAZ | CD1 | ILE- 1084 | 3.85 | 0 | Hydrophobic |
| FAE | CG1 | VAL- 1092 | 4.34 | 0 | Hydrophobic |
| CAR | CG2 | VAL- 1092 | 4.1 | 0 | Hydrophobic |
| FAE | CB | ALA- 1108 | 3.79 | 0 | Hydrophobic |
| FAD | CD1 | LEU- 1140 | 3.8 | 0 | Hydrophobic |
| FAC | CD2 | LEU- 1140 | 3.54 | 0 | Hydrophobic |
| FAD | CB | LEU- 1157 | 3.61 | 0 | Hydrophobic |
| FAE | CB | LEU- 1157 | 3.9 | 0 | Hydrophobic |
| CBJ | CD1 | LEU- 1157 | 4.03 | 0 | Hydrophobic |
| NAS | N | MET- 1160 | 3.07 | 152.53 | H-Bond (Protein Donor) |
| FAD | CG | MET- 1160 | 4.27 | 0 | Hydrophobic |
| CAF | CB | ASP- 1164 | 4.37 | 0 | Hydrophobic |
| CAK | SD | MET- 1211 | 4.39 | 0 | Hydrophobic |
| C5 | CE | MET- 1211 | 3.38 | 0 | Hydrophobic |
| CAH | SD | MET- 1211 | 4.17 | 0 | Hydrophobic |
| NBH | N | ASP- 1222 | 3.43 | 137.2 | H-Bond (Protein Donor) |
| OAA | N | ASP- 1222 | 3.13 | 144.78 | H-Bond (Protein Donor) |
| CAR | CE1 | TYR- 1230 | 3.85 | 0 | Hydrophobic |
| CAF | CB | TYR- 1230 | 3.71 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 1230 | 3.62 | 0 | Aromatic Face/Face |
