sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2006-02-13
| Name: | Ras-related C3 botulinum toxin substrate 3 |
|---|---|
| ID: | RAC3_HUMAN |
| AC: | P60763 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 12 % |
| B | 88 % |
| B-Factor: | 41.025 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CL MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.108 | 1309.500 |
| % Hydrophobic | % Polar |
|---|---|
| 41.75 | 58.25 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 63.67 % |
| Polar Surface area: | 276.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -11.7167 | -4.75864 | -19.1648 |
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 |
| O3B | N | ALA- 13 | 2.94 | 150.43 | H-Bond (Protein Donor) |
| O2B | N | GLY- 15 | 3.15 | 145.3 | H-Bond (Protein Donor) |
| O3A | N | GLY- 15 | 3.06 | 122.94 | H-Bond (Protein Donor) |
| O2B | N | LYS- 16 | 2.96 | 159.09 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 16 | 2.8 | 162.77 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 16 | 2.8 | 0 | Ionic (Protein Cationic) |
| O1B | N | THR- 17 | 3.18 | 156.48 | H-Bond (Protein Donor) |
| O1A | N | CYS- 18 | 2.74 | 158.03 | H-Bond (Protein Donor) |
| C2' | SG | CYS- 18 | 3.82 | 0 | Hydrophobic |
| C2' | CZ | PHE- 28 | 4.29 | 0 | Hydrophobic |
| C3' | CD1 | ILE- 33 | 3.62 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 118 | 2.83 | 161.6 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 118 | 3.45 | 138.89 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 118 | 2.95 | 165.16 | H-Bond (Ligand Donor) |
| O6 | OG | SER- 158 | 3.3 | 177.51 | H-Bond (Protein Donor) |
| O6 | N | ALA- 159 | 2.97 | 122.77 | H-Bond (Protein Donor) |
| O6 | N | LEU- 160 | 3.21 | 155.91 | H-Bond (Protein Donor) |
| O1B | MG | MG- 601 | 2.14 | 0 | Metal Acceptor |
