sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.710 Å
X-ray
2012-05-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.440 | 7.440 | 7.440 | 0.000 | 7.440 | 2 |
| Name: | BDNF/NT-3 growth factors receptor |
|---|---|
| ID: | NTRK2_HUMAN |
| AC: | Q16620 |
| 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: | 12.691 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.856 | 685.125 |
| % Hydrophobic | % Polar |
|---|---|
| 61.08 | 38.92 |
| According to VolSite | |
| HET Code: | MUJ |
|---|---|
| Formula: | C20H22N4O3 |
| Molecular weight: | 366.414 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.15 % |
| Polar Surface area: | 105.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -13.0169 | 28.0668 | -17.5404 |
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 |
| C7 | CD1 | LEU- 560 | 4.16 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 568 | 4.49 | 0 | Hydrophobic |
| C7 | CB | ALA- 586 | 3.74 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 608 | 4.02 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 608 | 3.75 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 611 | 3.7 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 616 | 3.79 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 617 | 4.39 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 617 | 4.41 | 0 | Hydrophobic |
| C22 | CB | VAL- 617 | 3.74 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 633 | 3.44 | 0 | Hydrophobic |
| C9 | CB | PHE- 633 | 4.13 | 0 | Hydrophobic |
| N26 | O | GLU- 634 | 2.89 | 147.04 | H-Bond (Ligand Donor) |
| N1 | N | MET- 636 | 3.33 | 149.07 | H-Bond (Protein Donor) |
| N27 | O | MET- 636 | 2.94 | 140.07 | H-Bond (Ligand Donor) |
| C25 | CD2 | LEU- 683 | 4.4 | 0 | Hydrophobic |
| C25 | CZ | PHE- 688 | 3.37 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 699 | 4.4 | 0 | Hydrophobic |
| C15 | CG | LEU- 699 | 3.7 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 699 | 3.97 | 0 | Hydrophobic |
| O16 | N | ASP- 710 | 2.86 | 166.82 | H-Bond (Protein Donor) |
| C20 | CB | ASP- 710 | 3.76 | 0 | Hydrophobic |
| C7 | CD2 | PHE- 711 | 3.73 | 0 | Hydrophobic |
| C12 | CB | PHE- 711 | 4.25 | 0 | Hydrophobic |
