sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2014-06-15
| Name: | Metallophosphoesterase |
|---|---|
| ID: | A3DJ38_CLOTH |
| AC: | A3DJ38 |
| Organism: | Clostridium thermocellum |
| Reign: | Bacteria |
| TaxID: | 203119 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.349 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.315 | 752.625 |
| % Hydrophobic | % Polar |
|---|---|
| 35.87 | 64.13 |
| According to VolSite | |
| HET Code: | GTP |
|---|---|
| Formula: | C10H12N5O14P3 |
| Molecular weight: | 519.149 g/mol |
| DrugBank ID: | DB04137 |
| Buried Surface Area: | 49.26 % |
| Polar Surface area: | 335.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| 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 |
|---|---|---|
| -32.3045 | 3.43581 | -8.49478 |
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 |
| O1G | OG | SER- 17 | 2.64 | 166.89 | H-Bond (Protein Donor) |
| O3B | N | GLY- 18 | 3.1 | 170.18 | H-Bond (Protein Donor) |
| O2B | N | GLY- 20 | 3.09 | 126.88 | H-Bond (Protein Donor) |
| O3A | N | GLY- 20 | 3.12 | 131.2 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 21 | 2.85 | 156.78 | H-Bond (Protein Donor) |
| O2B | N | LYS- 21 | 2.85 | 154.33 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 21 | 2.76 | 158.81 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 21 | 2.85 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 21 | 2.76 | 0 | Ionic (Protein Cationic) |
| O1B | N | SER- 22 | 3.01 | 161.15 | H-Bond (Protein Donor) |
| O2A | OG1 | THR- 23 | 2.79 | 158.27 | H-Bond (Protein Donor) |
| O2A | N | THR- 23 | 2.94 | 151.44 | H-Bond (Protein Donor) |
| C4' | CB | ARG- 116 | 4.14 | 0 | Hydrophobic |
| C1' | CD | ARG- 116 | 4.16 | 0 | Hydrophobic |
| O1G | NH1 | ARG- 120 | 2.88 | 160.87 | H-Bond (Protein Donor) |
| O1G | CZ | ARG- 120 | 3.9 | 0 | Ionic (Protein Cationic) |
| O1A | CZ | ARG- 120 | 3.77 | 0 | Ionic (Protein Cationic) |
| C5' | CD | ARG- 120 | 3.85 | 0 | Hydrophobic |
| C4' | CG | ARG- 120 | 4 | 0 | Hydrophobic |
| O1G | CZ | ARG- 123 | 3.61 | 0 | Ionic (Protein Cationic) |
| O3G | CZ | ARG- 123 | 3.71 | 0 | Ionic (Protein Cationic) |
| O1G | NH1 | ARG- 123 | 2.88 | 155.17 | H-Bond (Protein Donor) |
| O3G | NH2 | ARG- 123 | 2.8 | 167.02 | H-Bond (Protein Donor) |
| O3G | MG | MG- 1002 | 2.03 | 0 | Metal Acceptor |
| O1B | MG | MG- 1002 | 2.24 | 0 | Metal Acceptor |
