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
2011-05-05
| Name: | Chaperonin |
|---|---|
| ID: | Q877G8_METMI |
| AC: | Q877G8 |
| Organism: | Methanococcus maripaludis |
| Reign: | Archaea |
| TaxID: | 39152 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 49.170 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.763 | 658.125 |
| % Hydrophobic | % Polar |
|---|---|
| 48.21 | 51.79 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.76 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -28.7131 | 19.2087 | 26.9701 |
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' | CD1 | LEU- 39 | 3.88 | 0 | Hydrophobic |
| O1A | N | GLY- 40 | 2.87 | 155.63 | H-Bond (Protein Donor) |
| O5' | N | GLY- 40 | 3.24 | 134.75 | H-Bond (Protein Donor) |
| O3B | N | GLY- 92 | 3.07 | 123.61 | H-Bond (Protein Donor) |
| O1B | OG1 | THR- 94 | 3.33 | 139.32 | H-Bond (Protein Donor) |
| O1B | N | THR- 94 | 3.14 | 156.2 | H-Bond (Protein Donor) |
| O2B | N | THR- 95 | 2.63 | 158.17 | H-Bond (Protein Donor) |
| O2B | OG1 | THR- 95 | 2.68 | 157.1 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 161 | 3.57 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 161 | 3.05 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 161 | 3.05 | 159.21 | H-Bond (Protein Donor) |
| O2' | N | GLY- 404 | 2.67 | 139.7 | H-Bond (Protein Donor) |
| C4' | CD2 | LEU- 444 | 4.35 | 0 | Hydrophobic |
| C1' | CD2 | LEU- 444 | 4.14 | 0 | Hydrophobic |
| O2' | OE1 | GLU- 490 | 3.41 | 122.41 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 490 | 3.16 | 172.26 | H-Bond (Ligand Donor) |
| O3B | MG | MG- 544 | 2.58 | 0 | Metal Acceptor |
| O2A | MG | MG- 544 | 2.21 | 0 | Metal Acceptor |
| O2' | O | HOH- 550 | 3.17 | 120.69 | H-Bond (Protein Donor) |
