sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2012-11-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.220 | 8.220 | 8.220 | 0.000 | 8.220 | 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: | 17.979 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.148 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 69.39 | 30.61 |
| According to VolSite | |
| HET Code: | 6XE |
|---|---|
| Formula: | C20H13FN6 |
| Molecular weight: | 356.356 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.07 % |
| Polar Surface area: | 68.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 20.0986 | 10.6342 | 41.3611 |
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 | CD1 | ILE- 1084 | 3.84 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 1084 | 4.01 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 1092 | 4.26 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 1092 | 3.8 | 0 | Hydrophobic |
| C1 | CB | ALA- 1108 | 4.36 | 0 | Hydrophobic |
| C9 | CB | ALA- 1108 | 3.43 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 1157 | 3.93 | 0 | Hydrophobic |
| N3 | N | MET- 1160 | 2.93 | 156.68 | H-Bond (Protein Donor) |
| C9 | CG | MET- 1160 | 3.91 | 0 | Hydrophobic |
| C17 | CB | ASP- 1164 | 3.57 | 0 | Hydrophobic |
| C9 | CE | MET- 1211 | 4.25 | 0 | Hydrophobic |
| C18 | SD | MET- 1211 | 4.27 | 0 | Hydrophobic |
| C1 | CE | MET- 1211 | 3.58 | 0 | Hydrophobic |
| C1 | CE | MET- 1211 | 3.58 | 0 | Hydrophobic |
| N24 | N | ASP- 1222 | 2.85 | 143.5 | H-Bond (Protein Donor) |
| C27 | CZ | TYR- 1230 | 4.05 | 0 | Hydrophobic |
| C18 | CB | TYR- 1230 | 3.75 | 0 | Hydrophobic |
