sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.870 Å
X-ray
2011-08-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.890 | 8.890 | 8.890 | 0.000 | 8.890 | 1 |
| 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: | 19.832 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.144 | 523.125 |
| % Hydrophobic | % Polar |
|---|---|
| 56.13 | 43.87 |
| According to VolSite | |
| HET Code: | 6XP |
|---|---|
| Formula: | C18H18ClN3O3 |
| Molecular weight: | 359.807 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.62 % |
| Polar Surface area: | 90.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 19.1578 | 10.4024 | 5.032 |
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 |
| C5 | CG2 | ILE- 1084 | 3.97 | 0 | Hydrophobic |
| CL2 | CG2 | ILE- 1084 | 4.37 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 1092 | 4.31 | 0 | Hydrophobic |
| CL2 | CG2 | VAL- 1092 | 3.74 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 1092 | 3.94 | 0 | Hydrophobic |
| C3 | CB | ALA- 1108 | 3.55 | 0 | Hydrophobic |
| C4 | CB | ALA- 1108 | 3.48 | 0 | Hydrophobic |
| C50 | CB | LYS- 1110 | 4.5 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 1140 | 4.15 | 0 | Hydrophobic |
| C50 | CD1 | LEU- 1157 | 3.24 | 0 | Hydrophobic |
| C2 | CB | LEU- 1157 | 4.28 | 0 | Hydrophobic |
| C3 | CG | MET- 1160 | 3.82 | 0 | Hydrophobic |
| C4 | CB | MET- 1160 | 4.06 | 0 | Hydrophobic |
| O22 | N | MET- 1160 | 2.82 | 159.76 | H-Bond (Protein Donor) |
| C24 | CB | ASP- 1164 | 4.16 | 0 | Hydrophobic |
| C24 | CB | ARG- 1208 | 4.06 | 0 | Hydrophobic |
| N13 | O | ARG- 1208 | 2.63 | 144.35 | H-Bond (Ligand Donor) |
| C5 | CE | MET- 1211 | 3.77 | 0 | Hydrophobic |
| O21 | N | ASP- 1222 | 3.07 | 160.67 | H-Bond (Protein Donor) |
| C50 | CB | ALA- 1226 | 3.55 | 0 | Hydrophobic |
| C20 | CZ | TYR- 1230 | 4.16 | 0 | Hydrophobic |
| CL2 | CD1 | TYR- 1230 | 3.77 | 0 | Hydrophobic |
| C9 | CB | TYR- 1230 | 3.65 | 0 | Hydrophobic |
| C11 | CB | TYR- 1230 | 3.45 | 0 | Hydrophobic |
