sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2013-04-25
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 26.030 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.058 | 762.750 |
| % Hydrophobic | % Polar |
|---|---|
| 55.31 | 44.69 |
| According to VolSite | |
| HET Code: | STI |
|---|---|
| Formula: | C29H32N7O |
| Molecular weight: | 494.611 g/mol |
| DrugBank ID: | DB00619 |
| Buried Surface Area: | 64.76 % |
| Polar Surface area: | 87.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 13.1618 | -2.16146 | 9.61027 |
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 |
| C6 | CD1 | LEU- 616 | 4.4 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 624 | 4.1 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 624 | 4.4 | 0 | Hydrophobic |
| C5 | CB | ALA- 653 | 4.4 | 0 | Hydrophobic |
| C20 | CB | ALA- 653 | 3.81 | 0 | Hydrophobic |
| C17 | CD | LYS- 655 | 3.97 | 0 | Hydrophobic |
| C18 | CB | LYS- 655 | 3.39 | 0 | Hydrophobic |
| N21 | OE2 | GLU- 672 | 2.9 | 137.96 | H-Bond (Ligand Donor) |
| C25 | CG | GLU- 672 | 4.04 | 0 | Hydrophobic |
| C27 | CG2 | ILE- 675 | 4.34 | 0 | Hydrophobic |
| C15 | CE | MET- 676 | 3.93 | 0 | Hydrophobic |
| C23 | SD | MET- 676 | 4.36 | 0 | Hydrophobic |
| C25 | CG | MET- 676 | 4.11 | 0 | Hydrophobic |
| C17 | SD | MET- 676 | 3.59 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 679 | 3.96 | 0 | Hydrophobic |
| C29 | CG2 | ILE- 685 | 4.12 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 685 | 4.04 | 0 | Hydrophobic |
| C18 | CB | MET- 699 | 3.84 | 0 | Hydrophobic |
| C17 | SD | MET- 699 | 4.12 | 0 | Hydrophobic |
| N13 | OG1 | THR- 701 | 2.91 | 144.86 | H-Bond (Ligand Donor) |
| C20 | CG2 | THR- 701 | 3.98 | 0 | Hydrophobic |
| C14 | CG2 | THR- 701 | 3.54 | 0 | Hydrophobic |
| N3 | N | MET- 704 | 3.07 | 166.29 | H-Bond (Protein Donor) |
| N51 | O | VAL- 763 | 2.76 | 134.97 | H-Bond (Ligand Donor) |
| C5 | CD2 | LEU- 773 | 3.81 | 0 | Hydrophobic |
| O29 | N | ASP- 784 | 2.83 | 161.51 | H-Bond (Protein Donor) |
| C23 | CB | ASP- 784 | 3.67 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 785 | 3.92 | 0 | Aromatic Edge/Face |
