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
2007-03-07
| Name: | Ras-related C3 botulinum toxin substrate 1 |
|---|---|
| ID: | RAC1_HUMAN |
| AC: | P63000 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 6 % |
| C | 94 % |
| B-Factor: | 28.462 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.508 | 543.375 |
| % Hydrophobic | % Polar |
|---|---|
| 45.96 | 54.04 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 64.07 % |
| 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 |
|---|---|---|
| -30.1194 | 35.8983 | -5.83861 |
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 |
| O1B | N | ALA- 13 | 2.83 | 154.96 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 13 | 4.32 | 0 | Hydrophobic |
| O2B | N | GLY- 15 | 3.06 | 148.72 | H-Bond (Protein Donor) |
| O3A | N | GLY- 15 | 3.07 | 128.09 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 16 | 3.78 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 16 | 2.72 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 16 | 2.72 | 159.63 | H-Bond (Protein Donor) |
| O2B | N | LYS- 16 | 2.94 | 160.67 | H-Bond (Protein Donor) |
| O3B | N | THR- 17 | 2.92 | 160.58 | H-Bond (Protein Donor) |
| O1A | N | CYS- 18 | 2.77 | 162.47 | H-Bond (Protein Donor) |
| C2' | SG | CYS- 18 | 4.04 | 0 | Hydrophobic |
| C2' | CZ | PHE- 28 | 4.22 | 0 | Hydrophobic |
| C3' | CD1 | ILE- 33 | 3.55 | 0 | Hydrophobic |
| O3' | OD1 | ASN- 43 | 3.11 | 159.24 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 118 | 3.43 | 135.14 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 118 | 2.84 | 167.58 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 118 | 2.93 | 159.5 | H-Bond (Ligand Donor) |
| O6 | N | LEU- 160 | 3.08 | 156.61 | H-Bond (Protein Donor) |
| O3B | ZN | ZN- 201 | 2.18 | 0 | Metal Acceptor |
