sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2011-01-14
| Name: | Cell division control protein 42 homolog |
|---|---|
| ID: | CDC42_HUMAN |
| AC: | P60953 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 94 % |
| D | 6 % |
| B-Factor: | 47.814 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.053 | 300.375 |
| % Hydrophobic | % Polar |
|---|---|
| 41.57 | 58.43 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 56.82 % |
| 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 |
|---|---|---|
| -28.8951 | -26.6114 | 37.125 |
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 |
| O2B | N | ALA- 13 | 2.6 | 156.7 | H-Bond (Protein Donor) |
| O1B | N | GLY- 15 | 3.11 | 126.87 | H-Bond (Protein Donor) |
| O3A | N | GLY- 15 | 3.07 | 135.29 | H-Bond (Protein Donor) |
| O1B | N | LYS- 16 | 2.64 | 151.49 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 16 | 3.3 | 122.25 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 16 | 3.3 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 16 | 3.74 | 0 | Ionic (Protein Cationic) |
| O3B | N | THR- 17 | 3.09 | 163.74 | H-Bond (Protein Donor) |
| O2A | N | CYS- 18 | 2.52 | 174.72 | H-Bond (Protein Donor) |
| C5' | SG | CYS- 18 | 3.74 | 0 | Hydrophobic |
| C2' | SG | CYS- 18 | 4.15 | 0 | Hydrophobic |
| C3' | CB | VAL- 33 | 3.69 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 118 | 2.54 | 153.52 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 118 | 3.06 | 124.22 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 118 | 3.48 | 120.43 | H-Bond (Ligand Donor) |
