sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2015-02-18
| Name: | ATP phosphoribosyltransferase |
|---|---|
| ID: | HIS1_CAMJR |
| AC: | Q5HSJ4 |
| Organism: | Campylobacter jejuni |
| Reign: | Bacteria |
| TaxID: | 195099 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 94 % |
| C | 6 % |
| B-Factor: | 34.626 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.476 | 1113.750 |
| % Hydrophobic | % Polar |
|---|---|
| 27.58 | 72.42 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 55.64 % |
| 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 |
|---|---|---|
| -11.637 | 36.2364 | -33.8324 |
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 |
| O2G | NE2 | GLN- 12 | 3.03 | 169.29 | H-Bond (Protein Donor) |
| O2A | NE2 | GLN- 12 | 2.88 | 142.08 | H-Bond (Protein Donor) |
| O3A | NE2 | GLN- 12 | 3.44 | 125.53 | H-Bond (Protein Donor) |
| O1A | NH1 | ARG- 16 | 2.93 | 130.29 | H-Bond (Protein Donor) |
| O2A | N | ARG- 16 | 2.85 | 154.15 | H-Bond (Protein Donor) |
| C5' | CB | ARG- 16 | 4.4 | 0 | Hydrophobic |
| C1' | CD2 | LEU- 17 | 4.2 | 0 | Hydrophobic |
| C4' | CG | LEU- 17 | 3.96 | 0 | Hydrophobic |
| O1G | CZ | ARG- 54 | 3.27 | 0 | Ionic (Protein Cationic) |
| O2G | N | ASP- 55 | 3.18 | 179.03 | H-Bond (Protein Donor) |
| O3' | ND2 | ASN- 75 | 3.14 | 158.32 | H-Bond (Protein Donor) |
| O2' | OD1 | ASN- 75 | 2.61 | 151.84 | H-Bond (Ligand Donor) |
| C2' | SG | CYS- 104 | 3.54 | 0 | Hydrophobic |
| C3' | CD1 | LEU- 170 | 4 | 0 | Hydrophobic |
| O1G | MG | MG- 301 | 2.11 | 0 | Metal Acceptor |
| O2B | MG | MG- 301 | 1.9 | 0 | Metal Acceptor |
| O3' | O | HOH- 405 | 2.86 | 172.92 | H-Bond (Ligand Donor) |
