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
2009-06-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.080 | 9.280 | 9.190 | 0.210 | 9.570 | 3 |
| 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: | 36.056 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.564 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 62.79 | 37.21 |
| According to VolSite | |
| HET Code: | PFY |
|---|---|
| Formula: | C32H35Cl2N4O4S |
| Molecular weight: | 642.616 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 48.71 % |
| Polar Surface area: | 112.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 17.0958 | 10.8787 | 3.0413 |
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 |
| CL6 | CG2 | VAL- 1092 | 3.36 | 0 | Hydrophobic |
| C9 | CB | ALA- 1108 | 4.5 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 1140 | 4.05 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 1140 | 3.49 | 0 | Hydrophobic |
| C9 | CB | LEU- 1157 | 3.97 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 1157 | 4.01 | 0 | Hydrophobic |
| N19 | O | PRO- 1158 | 2.78 | 153.64 | H-Bond (Ligand Donor) |
| C28 | CZ | TYR- 1159 | 3.67 | 0 | Hydrophobic |
| O32 | N | MET- 1160 | 2.77 | 163.26 | H-Bond (Protein Donor) |
| C9 | CG | MET- 1160 | 4.42 | 0 | Hydrophobic |
| C17 | CG | MET- 1160 | 4.14 | 0 | Hydrophobic |
| C29 | CE | MET- 1211 | 3.86 | 0 | Hydrophobic |
| C17 | CG | MET- 1211 | 3.97 | 0 | Hydrophobic |
| C10 | SD | MET- 1211 | 3.51 | 0 | Hydrophobic |
| C7 | CG | MET- 1211 | 3.97 | 0 | Hydrophobic |
| C7 | CB | ALA- 1221 | 4.41 | 0 | Hydrophobic |
| O12 | N | ASP- 1222 | 2.81 | 142.61 | H-Bond (Protein Donor) |
| CL5 | CB | ASP- 1222 | 4.26 | 0 | Hydrophobic |
| C14 | CE2 | TYR- 1230 | 3.38 | 0 | Hydrophobic |
| CL6 | CZ | TYR- 1230 | 3.92 | 0 | Hydrophobic |
| CL5 | CD2 | TYR- 1230 | 3.76 | 0 | Hydrophobic |
| C3 | CB | TYR- 1230 | 4.01 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 1230 | 3.78 | 0 | Aromatic Face/Face |
