sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2015-08-02
| Name: | Nonspecific lipid-transfer protein, putative |
|---|---|
| ID: | C9ZUV7_TRYB9 |
| AC: | C9ZUV7 |
| Organism: | Trypanosoma brucei gambiense |
| Reign: | Eukaryota |
| TaxID: | 679716 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 5 % |
| D | 95 % |
| B-Factor: | 35.473 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.048 | 783.000 |
| % Hydrophobic | % Polar |
|---|---|
| 58.62 | 41.38 |
| According to VolSite | |
| HET Code: | MLC |
|---|---|
| Formula: | C24H33N7O19P3S |
| Molecular weight: | 848.541 g/mol |
| DrugBank ID: | DB04524 |
| Buried Surface Area: | 49 % |
| Polar Surface area: | 469.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 24 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 5 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 22 |
| X | Y | Z |
|---|---|---|
| -75.9242 | 5.05546 | -32.1023 |
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 |
| OM3 | N | GLY- 87 | 2.7 | 146.85 | H-Bond (Protein Donor) |
| CP7 | CE2 | PHE- 125 | 4.15 | 0 | Hydrophobic |
| CP4 | CZ | PHE- 125 | 3.69 | 0 | Hydrophobic |
| CP8 | CG | PRO- 141 | 3.83 | 0 | Hydrophobic |
| S | CG2 | ILE- 143 | 3.98 | 0 | Hydrophobic |
| O12 | CZ | ARG- 197 | 3.55 | 0 | Ionic (Protein Cationic) |
| CP9 | CG2 | VAL- 199 | 4.47 | 0 | Hydrophobic |
| CP8 | CG1 | VAL- 199 | 4.43 | 0 | Hydrophobic |
| C1' | CD2 | LEU- 205 | 4.42 | 0 | Hydrophobic |
| CP9 | CD1 | LEU- 205 | 3.64 | 0 | Hydrophobic |
| N6 | O | CYS- 208 | 2.71 | 149.25 | H-Bond (Ligand Donor) |
| CP4 | CB | ALA- 209 | 4.43 | 0 | Hydrophobic |
| O21 | NE | ARG- 211 | 2.78 | 121.08 | H-Bond (Protein Donor) |
| O21 | CZ | ARG- 211 | 3.2 | 0 | Ionic (Protein Cationic) |
| CM2 | CE2 | TYR- 297 | 4.32 | 0 | Hydrophobic |
| S | CB | CYS- 299 | 3.64 | 0 | Hydrophobic |
| S | CE2 | PHE- 300 | 4.46 | 0 | Hydrophobic |
| CP1 | CZ3 | TRP- 357 | 4.43 | 0 | Hydrophobic |
| OM3 | N | GLY- 395 | 2.97 | 161.35 | H-Bond (Protein Donor) |
