sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.630 Å
X-ray
2015-05-27
| Name: | Iron-sulfur cluster carrier protein |
|---|---|
| ID: | Q5JIH4_THEKO |
| AC: | Q5JIH4 |
| Organism: | Thermococcus kodakarensis ) |
| Reign: | Archaea |
| TaxID: | 69014 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 31.062 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.435 | 357.750 |
| % Hydrophobic | % Polar |
|---|---|
| 58.49 | 41.51 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.98 % |
| 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 |
|---|---|---|
| -1.49844 | 6.15152 | 31.7959 |
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 |
| O3B | N | GLY- 30 | 2.99 | 131.47 | H-Bond (Protein Donor) |
| O2B | N | VAL- 31 | 3.16 | 134.29 | H-Bond (Protein Donor) |
| O2B | N | GLY- 32 | 3.11 | 144.22 | H-Bond (Protein Donor) |
| O3A | N | GLY- 32 | 2.92 | 131.45 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 33 | 2.63 | 177.06 | H-Bond (Protein Donor) |
| O2B | N | LYS- 33 | 2.9 | 150.1 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 33 | 2.63 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 33 | 3.86 | 0 | Ionic (Protein Cationic) |
| O1B | N | SER- 34 | 2.94 | 147.9 | H-Bond (Protein Donor) |
| O2A | N | LEU- 35 | 2.88 | 156.97 | H-Bond (Protein Donor) |
| C2' | CD2 | LEU- 35 | 3.92 | 0 | Hydrophobic |
| N7 | ND2 | ASN- 187 | 2.98 | 157.95 | H-Bond (Protein Donor) |
| N6 | OD1 | ASN- 187 | 3.01 | 142.77 | H-Bond (Ligand Donor) |
| C1' | CE | MET- 188 | 3.97 | 0 | Hydrophobic |
| C4' | CE | MET- 188 | 4.37 | 0 | Hydrophobic |
| N6 | O | PRO- 217 | 2.95 | 147.93 | H-Bond (Ligand Donor) |
| N1 | N | TYR- 219 | 2.79 | 167.51 | H-Bond (Protein Donor) |
| O1B | MG | MG- 302 | 2.08 | 0 | Metal Acceptor |
