sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.310 Å
X-ray
2005-01-12
| Name: | Cytotoxin 3 |
|---|---|
| ID: | 3SA3_NAJAT |
| AC: | P60301 |
| Organism: | Naja atra |
| Reign: | Eukaryota |
| TaxID: | 8656 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 72 % |
| B | 28 % |
| B-Factor: | 32.680 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.507 | 661.500 |
| % Hydrophobic | % Polar |
|---|---|
| 46.43 | 53.57 |
| According to VolSite | |
| HET Code: | SFT |
|---|---|
| Formula: | C48H92NO12S |
| Molecular weight: | 907.309 g/mol |
| DrugBank ID: | DB04780 |
| Buried Surface Area: | 23.27 % |
| Polar Surface area: | 223.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 6 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 4 |
| Rotatable Bonds: | 43 |
| X | Y | Z |
|---|---|---|
| 41.5352 | -0.727839 | 28.0316 |
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 |
| C1 | CD | LYS- 12 | 3.9 | 0 | Hydrophobic |
| C3 | CD | LYS- 12 | 4.38 | 0 | Hydrophobic |
| O5' | NZ | LYS- 12 | 2.88 | 166.74 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 12 | 3.15 | 160.55 | H-Bond (Protein Donor) |
| C6' | CG | PRO- 15 | 4.09 | 0 | Hydrophobic |
| C3' | CG | PRO- 15 | 3.92 | 0 | Hydrophobic |
| C6 | CB | PRO- 15 | 3.93 | 0 | Hydrophobic |
| C42 | CB | PRO- 15 | 3.68 | 0 | Hydrophobic |
| O2B | NZ | LYS- 18 | 2.86 | 149.7 | H-Bond (Protein Donor) |
| C3' | CE | LYS- 18 | 3.53 | 0 | Hydrophobic |
| C3B | CE1 | TYR- 22 | 4.27 | 0 | Hydrophobic |
| O3S | NZ | LYS- 35 | 2.63 | 153.27 | H-Bond (Protein Donor) |
| O3S | NZ | LYS- 35 | 2.63 | 0 | Ionic (Protein Cationic) |
| O6' | O | ARG- 36 | 2.73 | 135.49 | H-Bond (Ligand Donor) |
| C1B | CB | CYS- 38 | 4.22 | 0 | Hydrophobic |
| O2B | O | CYS- 38 | 2.71 | 172.04 | H-Bond (Ligand Donor) |
| O2' | NZ | LYS- 44 | 2.8 | 146.72 | H-Bond (Protein Donor) |
| O1' | NZ | LYS- 44 | 3.06 | 134.08 | H-Bond (Protein Donor) |
| O3S | N | LYS- 44 | 2.93 | 154.62 | H-Bond (Protein Donor) |
| O2S | N | LYS- 44 | 3.25 | 135.13 | H-Bond (Protein Donor) |
| O2S | NZ | LYS- 44 | 3.81 | 0 | Ionic (Protein Cationic) |
| C4B | CD | LYS- 44 | 4 | 0 | Hydrophobic |
