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
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 |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 37.661 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.706 | 307.125 |
| % Hydrophobic | % Polar |
|---|---|
| 51.65 | 48.35 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.54 % |
| 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 |
|---|---|---|
| 21.0626 | 94.9584 | -19.5552 |
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 | 3.17 | 140.05 | H-Bond (Protein Donor) |
| O1B | NE2 | HIS- 54 | 2.64 | 156.27 | H-Bond (Protein Donor) |
| C2' | CB | HIS- 54 | 4.16 | 0 | Hydrophobic |
| N6 | OD2 | ASP- 81 | 2.79 | 153.21 | H-Bond (Ligand Donor) |
| C1' | CD1 | ILE- 86 | 3.97 | 0 | Hydrophobic |
| C1' | CB | ALA- 92 | 4.01 | 0 | Hydrophobic |
| C4' | CB | ALA- 92 | 3.96 | 0 | Hydrophobic |
| O3B | N | GLY- 107 | 2.8 | 150.97 | H-Bond (Protein Donor) |
| O2A | N | PHE- 110 | 3.02 | 167.66 | H-Bond (Protein Donor) |
| C1' | CE1 | PHE- 110 | 4.43 | 0 | Hydrophobic |
| C5' | CE1 | PHE- 110 | 3.79 | 0 | Hydrophobic |
| O3B | O | HOH- 149 | 2.78 | 138.66 | H-Bond (Protein Donor) |
| O1B | MG | MG- 602 | 2.37 | 0 | Metal Acceptor |
| O1A | MG | MG- 602 | 2.57 | 0 | Metal Acceptor |
