sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2014-02-17
| Name: | Ammonium transporter |
|---|---|
| ID: | B8ZYW1_HALMT |
| AC: | B8ZYW1 |
| Organism: | Haloferax mediterranei |
| Reign: | Archaea |
| TaxID: | 523841 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 44 % |
| C | 56 % |
| B-Factor: | 44.171 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.932 | 641.250 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 65.07 % |
| 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 |
|---|---|---|
| -33.8109 | 26.4987 | -15.371 |
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 |
| C4' | CG2 | ILE- 18 | 4.2 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 18 | 3.72 | 0 | Hydrophobic |
| O2' | OG1 | THR- 40 | 2.8 | 171.62 | H-Bond (Ligand Donor) |
| N3 | OG1 | THR- 40 | 2.74 | 140.92 | H-Bond (Protein Donor) |
| O2B | N | SER- 49 | 3.2 | 155.38 | H-Bond (Protein Donor) |
| C5' | CD | LYS- 69 | 4.45 | 0 | Hydrophobic |
| C4' | CG | LYS- 69 | 4.19 | 0 | Hydrophobic |
| N6 | O | VAL- 75 | 2.87 | 159.01 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 75 | 3.04 | 168.81 | H-Bond (Protein Donor) |
| O3A | N | GLY- 98 | 3.33 | 129.59 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 101 | 3.8 | 0 | Ionic (Protein Cationic) |
| N7 | NZ | LYS- 101 | 3.14 | 159.61 | H-Bond (Protein Donor) |
| O2G | NE2 | GLN- 112 | 3.3 | 142.44 | H-Bond (Protein Donor) |
| O3G | CZ | ARG- 114 | 3.89 | 0 | Ionic (Protein Cationic) |
| O3G | NH2 | ARG- 114 | 2.85 | 158.38 | H-Bond (Protein Donor) |
