sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2014-07-07
| Name: | Cyclic GMP-AMP synthase |
|---|---|
| ID: | DNCV_VIBCH |
| AC: | Q9KVG7 |
| Organism: | Vibrio cholerae serotype O1 |
| Reign: | Bacteria |
| TaxID: | 243277 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 49.924 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.015 | 486.000 |
| % Hydrophobic | % Polar |
|---|---|
| 32.64 | 67.36 |
| According to VolSite | |
| HET Code: | G2P |
|---|---|
| Formula: | C11H14N5O13P3 |
| Molecular weight: | 517.176 g/mol |
| DrugBank ID: | DB03532 |
| Buried Surface Area: | 51.37 % |
| Polar Surface area: | 326.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -4.19638 | 18.793 | -94.5814 |
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 |
| O4' | NE2 | GLN- 113 | 3.49 | 148.5 | H-Bond (Protein Donor) |
| C4' | CG | GLN- 113 | 3.73 | 0 | Hydrophobic |
| O2B | N | SER- 115 | 2.77 | 147.97 | H-Bond (Protein Donor) |
| O1B | OH | TYR- 118 | 3.06 | 158.55 | H-Bond (Protein Donor) |
| O3' | OH | TYR- 118 | 3.22 | 170.44 | H-Bond (Ligand Donor) |
| C2' | CG2 | VAL- 265 | 4.3 | 0 | Hydrophobic |
| O3G | NZ | LYS- 288 | 2.55 | 163.84 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 288 | 2.55 | 0 | Ionic (Protein Cationic) |
| O1G | OG | SER- 302 | 3.21 | 156.82 | H-Bond (Protein Donor) |
| O3B | OG | SER- 302 | 3.26 | 135.15 | H-Bond (Protein Donor) |
| C3A | CB | SER- 302 | 4.46 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 349 | 3.25 | 134.75 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 349 | 3.4 | 129.6 | H-Bond (Ligand Donor) |
| O2G | MG | MG- 502 | 2.39 | 0 | Metal Acceptor |
| O2B | MG | MG- 502 | 2.23 | 0 | Metal Acceptor |
| O2A | MG | MG- 502 | 2.19 | 0 | Metal Acceptor |
