sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2011-09-01
| Name: | Candidapepsin-1 |
|---|---|
| ID: | CARP1_CANPA |
| AC: | P32951 |
| Organism: | Candida parapsilosis |
| Reign: | Eukaryota |
| TaxID: | 5480 |
| EC Number: | 3.4.23.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 46.097 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.123 | 1512.000 |
| % Hydrophobic | % Polar |
|---|---|
| 34.60 | 65.40 |
| According to VolSite | |
| HET Code: | RIT |
|---|---|
| Formula: | C37H48N6O5S2 |
| Molecular weight: | 720.944 g/mol |
| DrugBank ID: | DB00503 |
| Buried Surface Area: | 51.94 % |
| Polar Surface area: | 202.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 9.14294 | -20.6385 | -26.6321 |
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 |
| S81 | CB | PRO- 12 | 4.14 | 0 | Hydrophobic |
| C86 | CG | PRO- 12 | 3.93 | 0 | Hydrophobic |
| C90 | CB | PRO- 12 | 4.41 | 0 | Hydrophobic |
| C48 | CD1 | ILE- 30 | 3.59 | 0 | Hydrophobic |
| S3 | CG1 | ILE- 76 | 3.86 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 76 | 4.42 | 0 | Hydrophobic |
| C6 | CD1 | TYR- 78 | 3.88 | 0 | Hydrophobic |
| C14 | CD1 | TYR- 78 | 3.76 | 0 | Hydrophobic |
| C52 | CB | TYR- 78 | 3.82 | 0 | Hydrophobic |
| O24 | N | GLY- 79 | 3.47 | 133.38 | H-Bond (Protein Donor) |
| O61 | N | ASP- 80 | 3.34 | 129.52 | H-Bond (Protein Donor) |
| C51 | CB | SER- 82 | 3.64 | 0 | Hydrophobic |
| C49 | CG1 | VAL- 113 | 3.75 | 0 | Hydrophobic |
| C48 | CD1 | ILE- 117 | 4.08 | 0 | Hydrophobic |
| S3 | CB | ALA- 127 | 4.32 | 0 | Hydrophobic |
| C35 | CD2 | LEU- 218 | 4.13 | 0 | Hydrophobic |
| O41 | OD1 | ASP- 220 | 2.54 | 141.64 | H-Bond (Ligand Donor) |
| O41 | OD2 | ASP- 220 | 2.89 | 146.92 | H-Bond (Ligand Donor) |
| N58 | O | GLY- 222 | 2.86 | 151.89 | H-Bond (Ligand Donor) |
| C64 | CB | THR- 223 | 4.19 | 0 | Hydrophobic |
| C68 | CG2 | THR- 223 | 4.24 | 0 | Hydrophobic |
| O76 | N | THR- 224 | 3.06 | 147.46 | H-Bond (Protein Donor) |
| C68 | CZ | TYR- 227 | 3.64 | 0 | Hydrophobic |
| C64 | CD1 | ILE- 303 | 3.71 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 303 | 3.69 | 0 | Hydrophobic |
