sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.210 Å
X-ray
2014-03-12
| Name: | CinA-like protein |
|---|---|
| ID: | Q5SHB0_THET8 |
| AC: | Q5SHB0 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 14 % |
| B | 86 % |
| B-Factor: | 29.424 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.071 | 1410.750 |
| % Hydrophobic | % Polar |
|---|---|
| 48.09 | 51.91 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 68.67 % |
| 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 |
|---|---|---|
| 33.7141 | 47.0098 | 13.8102 |
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 |
| C2' | CG2 | THR- 18 | 4.01 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 20 | 2.99 | 161.34 | H-Bond (Ligand Donor) |
| N1 | N | THR- 21 | 3.19 | 142.31 | H-Bond (Protein Donor) |
| N1 | N | ASN- 22 | 3.31 | 164.1 | H-Bond (Protein Donor) |
| O1A | N | GLY- 69 | 2.92 | 150.79 | H-Bond (Protein Donor) |
| O1B | N | LEU- 70 | 2.97 | 165.44 | H-Bond (Protein Donor) |
| O1B | N | GLY- 152 | 2.88 | 153.8 | H-Bond (Protein Donor) |
| O3A | N | GLY- 152 | 3.32 | 132.74 | H-Bond (Protein Donor) |
| C5' | CG | PRO- 153 | 3.65 | 0 | Hydrophobic |
| O3G | OE2 | GLU- 156 | 2.61 | 147.4 | H-Bond (Protein Donor) |
| O3' | O | PRO- 210 | 2.73 | 163.08 | H-Bond (Ligand Donor) |
| O2B | MG | MG- 401 | 2.07 | 0 | Metal Acceptor |
| O2A | MG | MG- 401 | 1.96 | 0 | Metal Acceptor |
