sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2008-11-11
| 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: | 30.455 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.480 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 68.42 | 31.58 |
| According to VolSite | |
| HET Code: | 353 |
|---|---|
| Formula: | C25H19ClF2N4O4 |
| Molecular weight: | 512.893 g/mol |
| DrugBank ID: | DB12064 |
| Buried Surface Area: | 76.65 % |
| Polar Surface area: | 106.78 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 0.624667 | 6.57339 | 56.196 |
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 | CG2 | ILE- 1084 | 3.95 | 0 | Hydrophobic |
| CL36 | CB | ILE- 1084 | 4.45 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 1092 | 4.35 | 0 | Hydrophobic |
| F35 | CG2 | VAL- 1092 | 3.31 | 0 | Hydrophobic |
| F35 | CB | ALA- 1108 | 4.33 | 0 | Hydrophobic |
| C7 | CB | ALA- 1108 | 3.42 | 0 | Hydrophobic |
| C8 | CD | LYS- 1110 | 3.88 | 0 | Hydrophobic |
| F35 | CB | LYS- 1110 | 3.84 | 0 | Hydrophobic |
| O31 | NZ | LYS- 1110 | 2.87 | 123.86 | H-Bond (Protein Donor) |
| O33 | NZ | LYS- 1110 | 3.25 | 158.72 | H-Bond (Protein Donor) |
| C24 | CE1 | PHE- 1124 | 3.6 | 0 | Hydrophobic |
| C25 | CB | GLU- 1127 | 3.54 | 0 | Hydrophobic |
| C2 | CG | MET- 1131 | 3.75 | 0 | Hydrophobic |
| F34 | CE2 | PHE- 1134 | 4.27 | 0 | Hydrophobic |
| F34 | CG1 | VAL- 1139 | 3.79 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 1140 | 3.85 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 1155 | 3.72 | 0 | Hydrophobic |
| F35 | CD1 | LEU- 1157 | 3.33 | 0 | Hydrophobic |
| N26 | N | MET- 1160 | 2.85 | 144.71 | H-Bond (Protein Donor) |
| N28 | O | MET- 1160 | 3 | 134.2 | H-Bond (Ligand Donor) |
| C14 | CD1 | LEU- 1195 | 4.32 | 0 | Hydrophobic |
| F34 | CD2 | LEU- 1195 | 3.92 | 0 | Hydrophobic |
| F34 | CE2 | PHE- 1200 | 4.19 | 0 | Hydrophobic |
| C4 | SD | MET- 1211 | 3.86 | 0 | Hydrophobic |
| C16 | CE | MET- 1211 | 3.48 | 0 | Hydrophobic |
| F34 | CG1 | VAL- 1220 | 3.7 | 0 | Hydrophobic |
| C3 | CB | ALA- 1221 | 4.11 | 0 | Hydrophobic |
| O30 | N | ASP- 1222 | 2.88 | 149.06 | H-Bond (Protein Donor) |
| C1 | CB | ASP- 1222 | 3.52 | 0 | Hydrophobic |
| CL36 | CZ | PHE- 1223 | 4.01 | 0 | Hydrophobic |
| C12 | CE1 | PHE- 1223 | 3.44 | 0 | Hydrophobic |
