sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.360 Å
X-ray
2012-05-03
| 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: | 27.661 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.030 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 64.12 | 35.88 |
| According to VolSite | |
| HET Code: | T6E |
|---|---|
| Formula: | C20H13F4N5OS |
| Molecular weight: | 447.409 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.74 % |
| Polar Surface area: | 121.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 56.7497 | 29.3689 | 19.2654 |
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 |
| S | CD1 | LEU- 560 | 3.81 | 0 | Hydrophobic |
| CAO | CG1 | VAL- 568 | 4.39 | 0 | Hydrophobic |
| C5 | CB | ALA- 586 | 3.69 | 0 | Hydrophobic |
| CAO | CB | ALA- 586 | 4.1 | 0 | Hydrophobic |
| CAM | CD | LYS- 588 | 3.69 | 0 | Hydrophobic |
| FAF | CD2 | LEU- 608 | 4.43 | 0 | Hydrophobic |
| F1 | CD1 | LEU- 608 | 4.08 | 0 | Hydrophobic |
| CAP | CD2 | LEU- 608 | 3.67 | 0 | Hydrophobic |
| FAF | CD2 | LEU- 611 | 3.38 | 0 | Hydrophobic |
| FAF | CG2 | ILE- 616 | 3.56 | 0 | Hydrophobic |
| CAP | CG1 | VAL- 617 | 4.48 | 0 | Hydrophobic |
| CAM | CB | PHE- 633 | 4.42 | 0 | Hydrophobic |
| NBF | O | GLU- 634 | 3 | 122.06 | H-Bond (Ligand Donor) |
| N3 | N | MET- 636 | 2.84 | 171.69 | H-Bond (Protein Donor) |
| FAF | CD2 | LEU- 683 | 3.93 | 0 | Hydrophobic |
| FAE | CD1 | LEU- 683 | 3.79 | 0 | Hydrophobic |
| CAK | CZ | PHE- 688 | 3.45 | 0 | Hydrophobic |
| FAE | CE2 | PHE- 688 | 3.46 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 699 | 4.08 | 0 | Hydrophobic |
| CAN | CD1 | LEU- 699 | 4.43 | 0 | Hydrophobic |
| FAG | CG2 | ILE- 708 | 4.29 | 0 | Hydrophobic |
| OAD | N | ASP- 710 | 2.81 | 163.06 | H-Bond (Protein Donor) |
| CAJ | CB | ASP- 710 | 3.7 | 0 | Hydrophobic |
| CAK | CB | ASP- 710 | 3.7 | 0 | Hydrophobic |
| S | CE2 | PHE- 711 | 3.75 | 0 | Hydrophobic |
| S | CE | MET- 713 | 4.12 | 0 | Hydrophobic |
