sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2009-04-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.400 | 8.770 | 8.700 | 0.280 | 9.260 | 5 |
| 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: | 34.555 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.135 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.24 | 44.76 |
| According to VolSite | |
| HET Code: | VGH |
|---|---|
| Formula: | C21H23Cl2FN5O |
| Molecular weight: | 451.345 g/mol |
| DrugBank ID: | DB08865 |
| Buried Surface Area: | 61.13 % |
| Polar Surface area: | 82.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 21.6961 | 83.7287 | 4.2816 |
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 |
| C9 | CG2 | ILE- 1084 | 4.08 | 0 | Hydrophobic |
| CL | CG2 | VAL- 1092 | 3.92 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 1092 | 3.76 | 0 | Hydrophobic |
| C15 | CB | ALA- 1108 | 3.7 | 0 | Hydrophobic |
| CL2 | CD2 | LEU- 1140 | 3.85 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 1157 | 3.69 | 0 | Hydrophobic |
| N22 | O | PRO- 1158 | 3.05 | 165.3 | H-Bond (Ligand Donor) |
| C20 | CZ | TYR- 1159 | 4.47 | 0 | Hydrophobic |
| N23 | N | MET- 1160 | 2.91 | 164.26 | H-Bond (Protein Donor) |
| F | CB | ASN- 1209 | 4.38 | 0 | Hydrophobic |
| CL2 | CG | MET- 1211 | 4.46 | 0 | Hydrophobic |
| C12 | SD | MET- 1211 | 3.56 | 0 | Hydrophobic |
| C4 | CE | MET- 1211 | 3.39 | 0 | Hydrophobic |
| C13 | CE | MET- 1211 | 4.22 | 0 | Hydrophobic |
| CL2 | CB | ALA- 1221 | 3.6 | 0 | Hydrophobic |
| F | CB | ALA- 1221 | 3.47 | 0 | Hydrophobic |
| F | CB | ASP- 1222 | 3.52 | 0 | Hydrophobic |
| CL2 | CB | ALA- 1226 | 4.05 | 0 | Hydrophobic |
| CL | CD1 | TYR- 1230 | 3.76 | 0 | Hydrophobic |
| C3 | CD2 | TYR- 1230 | 3.48 | 0 | Hydrophobic |
| C3 | CB | TYR- 1230 | 3.78 | 0 | Hydrophobic |
| C1 | CZ | TYR- 1230 | 3.85 | 0 | Hydrophobic |
