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
2011-08-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.300 | 8.300 | 8.300 | 0.000 | 8.300 | 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: | 22.652 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.846 | 401.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.42 | 49.58 |
| According to VolSite | |
| HET Code: | KRW |
|---|---|
| Formula: | C19H16N8O |
| Molecular weight: | 372.383 g/mol |
| DrugBank ID: | DB12848 |
| Buried Surface Area: | 69.97 % |
| Polar Surface area: | 107.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 19.7747 | 83.5057 | 4.43193 |
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 |
| C20 | CD1 | ILE- 1084 | 4.38 | 0 | Hydrophobic |
| C25 | CG1 | ILE- 1084 | 3.92 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 1084 | 3.76 | 0 | Hydrophobic |
| C | CG2 | VAL- 1092 | 4.09 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 1092 | 3.76 | 0 | Hydrophobic |
| C20 | CB | ALA- 1108 | 4.29 | 0 | Hydrophobic |
| C18 | CB | ALA- 1108 | 3.39 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 1157 | 3.9 | 0 | Hydrophobic |
| N22 | N | MET- 1160 | 2.9 | 163.49 | H-Bond (Protein Donor) |
| C18 | CG | MET- 1160 | 3.93 | 0 | Hydrophobic |
| C18 | CE | MET- 1211 | 4.28 | 0 | Hydrophobic |
| C20 | CE | MET- 1211 | 3.73 | 0 | Hydrophobic |
| C20 | CE | MET- 1211 | 3.73 | 0 | Hydrophobic |
| N7 | N | ASP- 1222 | 2.94 | 140.55 | H-Bond (Protein Donor) |
| C27 | CB | TYR- 1230 | 4.31 | 0 | Hydrophobic |
| C | CZ | TYR- 1230 | 3.9 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 1230 | 3.72 | 0 | Aromatic Face/Face |
| C27 | CB | ASP- 1231 | 3.59 | 0 | Hydrophobic |
| N13 | O | HOH- 2067 | 2.85 | 171.12 | H-Bond (Protein Donor) |
