sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-08-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.700 | 8.700 | 8.700 | 0.000 | 8.700 | 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: | 30.458 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.471 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 76.60 | 23.40 |
| According to VolSite | |
| HET Code: | DF6 |
|---|---|
| Formula: | C26H23N3O4S |
| Molecular weight: | 473.544 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.11 % |
| Polar Surface area: | 113.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 9.70997 | -16.4261 | -28.6873 |
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 |
| C34 | CG2 | ILE- 1084 | 3.93 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 1084 | 4.41 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 1084 | 3.31 | 0 | Hydrophobic |
| C32 | CG2 | ILE- 1084 | 3.78 | 0 | Hydrophobic |
| C29 | CG2 | VAL- 1092 | 4.29 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 1092 | 4.19 | 0 | Hydrophobic |
| C8 | CB | ALA- 1108 | 3.44 | 0 | Hydrophobic |
| C28 | CD | LYS- 1110 | 3.72 | 0 | Hydrophobic |
| N18 | O | GLU- 1127 | 2.84 | 163.61 | H-Bond (Ligand Donor) |
| C21 | CD1 | ILE- 1130 | 3.41 | 0 | Hydrophobic |
| C27 | CG | MET- 1131 | 3.65 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 1139 | 3.94 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 1140 | 3.42 | 0 | Hydrophobic |
| C8 | CB | LEU- 1157 | 4.22 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 1157 | 3.62 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 1157 | 3.37 | 0 | Hydrophobic |
| C1 | CZ | TYR- 1159 | 3.64 | 0 | Hydrophobic |
| C4 | CB | MET- 1160 | 4.19 | 0 | Hydrophobic |
| N6 | N | MET- 1160 | 3.11 | 146.57 | H-Bond (Protein Donor) |
| C25 | CD1 | LEU- 1195 | 4.03 | 0 | Hydrophobic |
| C12 | SD | MET- 1211 | 4.03 | 0 | Hydrophobic |
| C30 | CE | MET- 1211 | 3.28 | 0 | Hydrophobic |
| C30 | CE | MET- 1211 | 3.28 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 1220 | 4.12 | 0 | Hydrophobic |
| C13 | CB | ALA- 1221 | 4.3 | 0 | Hydrophobic |
| O20 | N | ASP- 1222 | 2.92 | 145.82 | H-Bond (Protein Donor) |
| C23 | CB | ASP- 1222 | 3.36 | 0 | Hydrophobic |
| C34 | CE2 | PHE- 1223 | 4 | 0 | Hydrophobic |
