sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.940 Å
X-ray
2015-06-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.160 | 9.160 | 9.160 | 0.000 | 9.160 | 2 |
| Name: | Epithelial discoidin domain-containing receptor 1 |
|---|---|
| ID: | DDR1_HUMAN |
| AC: | Q08345 |
| 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: | 42.453 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | IOD |
| Ligandability | Volume (Å3) |
|---|---|
| 1.352 | 1350.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.25 | 46.75 |
| According to VolSite | |
| HET Code: | 1N1 |
|---|---|
| Formula: | C22H27ClN7O2S |
| Molecular weight: | 489.013 g/mol |
| DrugBank ID: | DB01254 |
| Buried Surface Area: | 57.37 % |
| Polar Surface area: | 135.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 16.2346 | 38.0982 | 37.2766 |
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 |
| C12 | CD2 | LEU- 616 | 4.1 | 0 | Hydrophobic |
| C15 | CB | LEU- 616 | 4.19 | 0 | Hydrophobic |
| S | CD1 | LEU- 616 | 4.25 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 624 | 4.5 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 624 | 4.14 | 0 | Hydrophobic |
| S | CG1 | VAL- 624 | 4.41 | 0 | Hydrophobic |
| C10 | CB | ALA- 653 | 3.96 | 0 | Hydrophobic |
| C7 | CD | LYS- 655 | 3.93 | 0 | Hydrophobic |
| C10 | CB | LYS- 655 | 3.69 | 0 | Hydrophobic |
| C7 | SD | MET- 676 | 3.57 | 0 | Hydrophobic |
| CL | CG1 | ILE- 685 | 3.92 | 0 | Hydrophobic |
| C7 | SD | MET- 699 | 4 | 0 | Hydrophobic |
| C8 | CB | MET- 699 | 4.03 | 0 | Hydrophobic |
| N2 | OG1 | THR- 701 | 3.09 | 158.23 | H-Bond (Ligand Donor) |
| C5 | CG2 | THR- 701 | 4.12 | 0 | Hydrophobic |
| C9 | CG2 | THR- 701 | 3.44 | 0 | Hydrophobic |
| N | O | MET- 704 | 2.91 | 144.45 | H-Bond (Ligand Donor) |
| N1 | N | MET- 704 | 3.01 | 168.78 | H-Bond (Protein Donor) |
| S | CD2 | LEU- 773 | 4.03 | 0 | Hydrophobic |
| CL | CD1 | LEU- 773 | 3.9 | 0 | Hydrophobic |
| CL | CB | ALA- 783 | 3.51 | 0 | Hydrophobic |
| C15 | CZ | PHE- 785 | 4.06 | 0 | Hydrophobic |
| CL | CD1 | PHE- 785 | 3.81 | 0 | Hydrophobic |
