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
2004-03-05
| Name: | Diadenosine hexaphosphate hydrolase |
|---|---|
| ID: | NDX1_THETH |
| AC: | Q75UV1 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 274 |
| EC Number: | 3.6.1.61 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.059 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.135 | 718.875 |
| % Hydrophobic | % Polar |
|---|---|
| 42.25 | 57.75 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 48.34 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -44.7294 | 72.8509 | 101.834 |
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' | OD2 | ASP- 21 | 2.75 | 149.4 | H-Bond (Ligand Donor) |
| C2' | CD2 | PHE- 25 | 3.65 | 0 | Hydrophobic |
| O2B | NZ | LYS- 30 | 2.99 | 149.64 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 30 | 2.99 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 30 | 2.57 | 0 | Ionic (Protein Cationic) |
| O2A | OH | TYR- 66 | 3.1 | 156.71 | H-Bond (Protein Donor) |
| C5' | CE2 | TYR- 66 | 4.46 | 0 | Hydrophobic |
| O1A | ND2 | ASN- 68 | 2.92 | 160.64 | H-Bond (Protein Donor) |
| C4' | CB | ASN- 68 | 4.16 | 0 | Hydrophobic |
| C4' | CG | PRO- 69 | 4.47 | 0 | Hydrophobic |
| C1' | CG | PRO- 69 | 4.27 | 0 | Hydrophobic |
| O1G | CZ | ARG- 74 | 3.79 | 0 | Ionic (Protein Cationic) |
| O1A | CZ | ARG- 74 | 3.97 | 0 | Ionic (Protein Cationic) |
| O1A | NH1 | ARG- 74 | 2.83 | 146.87 | H-Bond (Protein Donor) |
| DuAr | DuAr | PHE- 110 | 3.51 | 0 | Aromatic Face/Face |
| C2' | CZ | PHE- 110 | 3.84 | 0 | Hydrophobic |
| N6 | OE1 | GLU- 112 | 3.16 | 152.08 | H-Bond (Ligand Donor) |
| N1 | O | HOH- 2012 | 2.73 | 179.99 | H-Bond (Protein Donor) |
