sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2008-10-14
| Name: | Hypothetical conserved protein |
|---|---|
| ID: | Q8KKW2_RHIEC |
| AC: | Q8KKW2 |
| Organism: | Rhizobium etli |
| Reign: | Bacteria |
| TaxID: | 347834 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 3 % |
| C | 97 % |
| B-Factor: | 38.374 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.047 | 516.375 |
| % Hydrophobic | % Polar |
|---|---|
| 54.90 | 45.10 |
| According to VolSite | |
| HET Code: | BTN |
|---|---|
| Formula: | C10H15N2O3S |
| Molecular weight: | 243.303 g/mol |
| DrugBank ID: | DB00121 |
| Buried Surface Area: | 77.42 % |
| Polar Surface area: | 106.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 7.04106 | 56.2403 | 33.5664 |
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 |
| O3 | ND2 | ASN- 21 | 3.01 | 166.18 | H-Bond (Protein Donor) |
| O3 | OG | SER- 25 | 2.59 | 142.54 | H-Bond (Protein Donor) |
| O3 | OH | TYR- 41 | 2.54 | 177.13 | H-Bond (Protein Donor) |
| N2 | OD1 | ASN- 43 | 3.03 | 169.52 | H-Bond (Ligand Donor) |
| C9 | CB | THR- 48 | 4.01 | 0 | Hydrophobic |
| C7 | CB | THR- 48 | 4.35 | 0 | Hydrophobic |
| O11 | N | GLY- 49 | 3.1 | 138.55 | H-Bond (Protein Donor) |
| C10 | CB | CYS- 50 | 4.17 | 0 | Hydrophobic |
| C10 | CD2 | TRP- 72 | 3.8 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 72 | 3.95 | 0 | Hydrophobic |
| S1 | CZ2 | TRP- 72 | 3.91 | 0 | Hydrophobic |
| C8 | CE2 | TRP- 72 | 3.53 | 0 | Hydrophobic |
| C10 | CB | CYS- 79 | 4.01 | 0 | Hydrophobic |
| O12 | OG | SER- 81 | 2.82 | 164.59 | H-Bond (Protein Donor) |
| S1 | CG2 | THR- 83 | 3.67 | 0 | Hydrophobic |
| C6 | CZ2 | TRP- 85 | 4.1 | 0 | Hydrophobic |
| C6 | CD2 | TRP- 102 | 3.39 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 104 | 4.36 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 104 | 4.39 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 119 | 2.73 | 173.59 | H-Bond (Ligand Donor) |
