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
2014-01-07
| 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: | 45.358 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.261 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 59.15 | 40.85 |
| According to VolSite | |
| HET Code: | DI1 |
|---|---|
| Formula: | C30H32F3N4O3 |
| Molecular weight: | 553.595 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.62 % |
| Polar Surface area: | 75.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 1.1104 | 33.9327 | 12.779 |
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 |
| C32 | CD1 | LEU- 616 | 4.36 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 624 | 4.19 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 624 | 3.54 | 0 | Hydrophobic |
| C26 | CB | ALA- 653 | 3.82 | 0 | Hydrophobic |
| C32 | CB | ALA- 653 | 4.39 | 0 | Hydrophobic |
| C34 | CB | ALA- 653 | 3.61 | 0 | Hydrophobic |
| C23 | CD | LYS- 655 | 4.18 | 0 | Hydrophobic |
| C26 | CB | LYS- 655 | 3.53 | 0 | Hydrophobic |
| C27 | CD | LYS- 655 | 3.81 | 0 | Hydrophobic |
| N21 | OE2 | GLU- 672 | 2.91 | 146.27 | H-Bond (Ligand Donor) |
| C12 | CG | GLU- 672 | 3.92 | 0 | Hydrophobic |
| C23 | CE | MET- 676 | 4.13 | 0 | Hydrophobic |
| C13 | SD | MET- 676 | 3.61 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 679 | 4.2 | 0 | Hydrophobic |
| F18 | CG2 | ILE- 684 | 3.76 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 685 | 4.06 | 0 | Hydrophobic |
| F18 | CG2 | ILE- 685 | 4.3 | 0 | Hydrophobic |
| C35 | CD1 | ILE- 685 | 4.17 | 0 | Hydrophobic |
| C23 | SD | MET- 699 | 4.16 | 0 | Hydrophobic |
| C24 | CB | MET- 699 | 3.99 | 0 | Hydrophobic |
| C24 | CG2 | THR- 701 | 3.44 | 0 | Hydrophobic |
| O38 | N | MET- 704 | 2.63 | 169.71 | H-Bond (Protein Donor) |
| F17 | CD2 | LEU- 757 | 3.54 | 0 | Hydrophobic |
| F19 | CD1 | LEU- 757 | 3.73 | 0 | Hydrophobic |
| N03 | O | VAL- 763 | 2.69 | 139.45 | H-Bond (Ligand Donor) |
| C01 | CG | ARG- 765 | 3.79 | 0 | Hydrophobic |
| C35 | CD1 | LEU- 773 | 3.51 | 0 | Hydrophobic |
| F18 | CG2 | ILE- 782 | 3.89 | 0 | Hydrophobic |
| F19 | CG2 | ILE- 782 | 4.07 | 0 | Hydrophobic |
| F19 | CB | ASP- 784 | 4.25 | 0 | Hydrophobic |
| C13 | CB | ASP- 784 | 3.62 | 0 | Hydrophobic |
| O40 | N | ASP- 784 | 2.93 | 166.57 | H-Bond (Protein Donor) |
| C31 | CE | MET- 787 | 4.05 | 0 | Hydrophobic |
