sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2014-01-18
| Name: | Protein clpf-1 |
|---|---|
| ID: | CLP1_CAEEL |
| AC: | P52874 |
| Organism: | Caenorhabditis elegans |
| Reign: | Eukaryota |
| TaxID: | 6239 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.564 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.361 | 2237.625 |
| % Hydrophobic | % Polar |
|---|---|
| 39.97 | 60.03 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.92 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -5.09426 | 19.611 | 6.49085 |
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 |
| N6 | OE2 | GLU- 16 | 3.05 | 165.59 | H-Bond (Ligand Donor) |
| O2' | O | ARG- 56 | 2.86 | 150.01 | H-Bond (Ligand Donor) |
| C1' | CB | ARG- 56 | 4.05 | 0 | Hydrophobic |
| O1B | N | ASP- 124 | 3.28 | 146.9 | H-Bond (Protein Donor) |
| O3B | N | VAL- 125 | 2.97 | 148.34 | H-Bond (Protein Donor) |
| O3A | N | GLY- 126 | 3.27 | 133.57 | H-Bond (Protein Donor) |
| O3B | N | LYS- 127 | 2.91 | 161.54 | H-Bond (Protein Donor) |
| O2B | N | THR- 128 | 3.13 | 169.88 | H-Bond (Protein Donor) |
| O1A | OG1 | THR- 129 | 2.85 | 159.8 | H-Bond (Protein Donor) |
| O1A | N | THR- 129 | 3.02 | 149.4 | H-Bond (Protein Donor) |
| C5' | CG1 | VAL- 285 | 4.18 | 0 | Hydrophobic |
| O2A | NH1 | ARG- 288 | 3.42 | 120.57 | H-Bond (Protein Donor) |
| O2B | MG | MG- 502 | 1.99 | 0 | Metal Acceptor |
