sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2004-04-01
| Name: | Cell division control protein 2 homolog |
|---|---|
| ID: | CDC2H_PLAFK |
| AC: | Q07785 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 5839 |
| EC Number: | 2.7.11.22 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.429 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.955 | 604.125 |
| % Hydrophobic | % Polar |
|---|---|
| 54.19 | 45.81 |
| According to VolSite | |
| HET Code: | PVB |
|---|---|
| Formula: | C20H24ClN6O3 |
| Molecular weight: | 431.896 g/mol |
| DrugBank ID: | DB02733 |
| Buried Surface Area: | 58.44 % |
| Polar Surface area: | 128.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 25.7205 | -1.5212 | 34.8997 |
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 |
| C13 | CG2 | ILE- 10 | 4.18 | 0 | Hydrophobic |
| C2A | CG2 | ILE- 10 | 3.64 | 0 | Hydrophobic |
| C16 | CB | VAL- 18 | 3.84 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 18 | 3.77 | 0 | Hydrophobic |
| C11 | CB | ALA- 30 | 3.79 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 63 | 3.86 | 0 | Hydrophobic |
| C9 | CB | PHE- 79 | 3.85 | 0 | Hydrophobic |
| C11 | CD1 | PHE- 79 | 3.8 | 0 | Hydrophobic |
| C10 | CG | PHE- 79 | 4.21 | 0 | Hydrophobic |
| N7 | N | LEU- 82 | 3.01 | 168.17 | H-Bond (Protein Donor) |
| N6 | O | LEU- 82 | 2.76 | 161.57 | H-Bond (Ligand Donor) |
| CL1 | CB | ASP- 85 | 4.29 | 0 | Hydrophobic |
| C15 | CB | ASP- 85 | 4.11 | 0 | Hydrophobic |
| O1 | OD1 | ASP- 85 | 3.42 | 133.56 | H-Bond (Ligand Donor) |
| OX1 | NZ | LYS- 88 | 3.91 | 0 | Ionic (Protein Cationic) |
| O1 | O | GLN- 129 | 2.59 | 121.68 | H-Bond (Ligand Donor) |
| C10 | CD1 | LEU- 132 | 3.73 | 0 | Hydrophobic |
| C10 | CB | ALA- 142 | 3.42 | 0 | Hydrophobic |
