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
2003-02-11
| Name: | Transcriptional regulator (NtrC family) |
|---|---|
| ID: | O67198_AQUAE |
| AC: | O67198 |
| Organism: | Aquifex aeolicus |
| Reign: | Bacteria |
| TaxID: | 224324 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 6 % |
| B | 94 % |
| B-Factor: | 61.637 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.006 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 48.65 | 51.35 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.96 % |
| 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 |
|---|---|---|
| -32.0447 | -21.5499 | -1.16993 |
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 | O | VAL- 140 | 2.76 | 135.21 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 140 | 2.7 | 153.62 | H-Bond (Protein Donor) |
| O1B | N | GLY- 170 | 3.27 | 120.4 | H-Bond (Protein Donor) |
| O3B | N | GLY- 170 | 2.85 | 156.94 | H-Bond (Protein Donor) |
| O1B | N | VAL- 171 | 3.11 | 124.55 | H-Bond (Protein Donor) |
| O1B | N | GLY- 172 | 3.17 | 144.89 | H-Bond (Protein Donor) |
| O3A | N | GLY- 172 | 3.13 | 140.59 | H-Bond (Protein Donor) |
| O1B | N | LYS- 173 | 3.13 | 165.93 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 173 | 3.16 | 146.14 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 173 | 3.16 | 0 | Ionic (Protein Cationic) |
| O2B | N | GLU- 174 | 3.15 | 151.14 | H-Bond (Protein Donor) |
| O1A | N | VAL- 175 | 3.15 | 144.93 | H-Bond (Protein Donor) |
| C2' | CG2 | VAL- 175 | 3.68 | 0 | Hydrophobic |
| C1' | CZ | PHE- 324 | 4.22 | 0 | Hydrophobic |
| C4' | CG1 | VAL- 356 | 4.46 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 356 | 3.77 | 0 | Hydrophobic |
| C5' | CB | ARG- 357 | 3.88 | 0 | Hydrophobic |
| O3' | NZ | LYS- 360 | 2.96 | 173.28 | H-Bond (Protein Donor) |
| O3B | O | HOH- 677 | 2.94 | 179.96 | H-Bond (Protein Donor) |
