sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2012-03-28
| 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: | 32.487 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.578 | 853.875 |
| % Hydrophobic | % Polar |
|---|---|
| 64.03 | 35.97 |
| According to VolSite | |
| HET Code: | L1X |
|---|---|
| Formula: | C30H22F2N6O3 |
| Molecular weight: | 552.531 g/mol |
| DrugBank ID: | DB12381 |
| Buried Surface Area: | 65.18 % |
| Polar Surface area: | 105.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 11.798 | -1.30471 | 44.9414 |
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 |
| C30 | CG2 | ILE- 1084 | 4.21 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 1084 | 3.28 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 1092 | 4.25 | 0 | Hydrophobic |
| F41 | CG1 | VAL- 1092 | 4.15 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 1092 | 4.13 | 0 | Hydrophobic |
| C13 | CB | ALA- 1108 | 3.78 | 0 | Hydrophobic |
| F41 | CD | LYS- 1110 | 3.53 | 0 | Hydrophobic |
| C29 | CG2 | ILE- 1130 | 3.59 | 0 | Hydrophobic |
| C29 | CG | MET- 1131 | 3.75 | 0 | Hydrophobic |
| C2 | CG | MET- 1131 | 3.74 | 0 | Hydrophobic |
| C29 | CE2 | PHE- 1134 | 4.16 | 0 | Hydrophobic |
| F40 | CE2 | PHE- 1134 | 4.35 | 0 | Hydrophobic |
| F40 | CG1 | VAL- 1139 | 3.83 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 1140 | 4.1 | 0 | Hydrophobic |
| C6 | CB | LEU- 1140 | 4.34 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 1157 | 4.32 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 1157 | 3.48 | 0 | Hydrophobic |
| C30 | CE1 | TYR- 1159 | 3.53 | 0 | Hydrophobic |
| C30 | CB | MET- 1160 | 4.43 | 0 | Hydrophobic |
| N31 | N | MET- 1160 | 2.89 | 159.08 | H-Bond (Protein Donor) |
| F40 | CD1 | LEU- 1195 | 3.23 | 0 | Hydrophobic |
| C4 | CE | MET- 1211 | 3.86 | 0 | Hydrophobic |
| C7 | SD | MET- 1211 | 3.84 | 0 | Hydrophobic |
| C16 | SD | MET- 1211 | 4.09 | 0 | Hydrophobic |
| F40 | CG1 | VAL- 1220 | 3.49 | 0 | Hydrophobic |
| O37 | N | ASP- 1222 | 2.89 | 154.83 | H-Bond (Protein Donor) |
| C1 | CB | ASP- 1222 | 3.61 | 0 | Hydrophobic |
