sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2004-06-01
| Name: | Anti-sigma F factor |
|---|---|
| ID: | SP2AB_GEOSE |
| AC: | O32727 |
| Organism: | Geobacillus stearothermophilus |
| Reign: | Bacteria |
| TaxID: | 1422 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 98 % |
| D | 2 % |
| B-Factor: | 41.315 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.119 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.39 | 41.61 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.92 % |
| 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 |
|---|---|---|
| 8.43804 | 26.4116 | 89.0271 |
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 |
| O1A | ND2 | ASN- 50 | 2.94 | 154.95 | H-Bond (Protein Donor) |
| O1B | NE2 | HIS- 54 | 3.07 | 144.89 | H-Bond (Protein Donor) |
| O2B | NE2 | HIS- 54 | 3.01 | 142.35 | H-Bond (Protein Donor) |
| N6 | OD2 | ASP- 81 | 3.37 | 141.9 | H-Bond (Ligand Donor) |
| C1' | CG1 | ILE- 86 | 4.23 | 0 | Hydrophobic |
| C4' | CE2 | PHE- 97 | 3.68 | 0 | Hydrophobic |
| O2B | OG1 | THR- 98 | 2.76 | 172.82 | H-Bond (Protein Donor) |
| O3' | OG1 | THR- 98 | 3.47 | 123.17 | H-Bond (Ligand Donor) |
| O3' | OG1 | THR- 99 | 3.12 | 145.27 | H-Bond (Protein Donor) |
| O3' | N | THR- 99 | 3.21 | 166.58 | H-Bond (Protein Donor) |
| C2' | CG2 | THR- 99 | 4.35 | 0 | Hydrophobic |
| O2' | OG1 | THR- 99 | 2.82 | 168.62 | H-Bond (Ligand Donor) |
| O3B | CZ | ARG- 105 | 3.6 | 0 | Ionic (Protein Cationic) |
| O3B | N | GLY- 107 | 3.2 | 147.8 | H-Bond (Protein Donor) |
| O2A | N | PHE- 110 | 2.99 | 172.71 | H-Bond (Protein Donor) |
| C5' | CD1 | PHE- 110 | 4.46 | 0 | Hydrophobic |
