sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.250 Å
X-ray
2014-05-15
| Name: | Uncharacterized protein |
|---|---|
| ID: | Q38AM1_TRYB2 |
| AC: | Q38AM1 |
| Organism: | Trypanosoma brucei brucei |
| Reign: | Eukaryota |
| TaxID: | 185431 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 20.288 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.222 | 813.375 |
| % Hydrophobic | % Polar |
|---|---|
| 53.53 | 46.47 |
| According to VolSite | |
| HET Code: | 1GH |
|---|---|
| Formula: | C23H21N5O3 |
| Molecular weight: | 415.445 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.78 % |
| Polar Surface area: | 93.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 46.5347 | 42.7532 | 22.2393 |
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 |
| C21 | CD2 | LEU- 16 | 4.01 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 19 | 3.67 | 0 | Hydrophobic |
| C11 | CB | SER- 20 | 4.49 | 0 | Hydrophobic |
| C1 | CB | SER- 20 | 4.06 | 0 | Hydrophobic |
| C2 | CB | SER- 20 | 3.41 | 0 | Hydrophobic |
| C1 | CB | TRP- 23 | 4.18 | 0 | Hydrophobic |
| C23 | CE2 | TRP- 23 | 3.51 | 0 | Hydrophobic |
| C11 | CB | ASP- 24 | 3.79 | 0 | Hydrophobic |
| C6 | CB | MET- 30 | 4.19 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 35 | 4.11 | 0 | Hydrophobic |
| C23 | CB | GLU- 39 | 3.63 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 40 | 4.12 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 40 | 3.88 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 40 | 3.8 | 0 | Hydrophobic |
| C21 | CG | ARG- 57 | 3.95 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 86 | 3.31 | 166.46 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 86 | 2.66 | 161.53 | H-Bond (Ligand Donor) |
| N2 | NE1 | TRP- 92 | 3.14 | 126.49 | H-Bond (Protein Donor) |
| DuAr | DuAr | TRP- 92 | 3.84 | 0 | Aromatic Face/Face |
