sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2002-08-28
| Name: | MutT/nudix family protein |
|---|---|
| ID: | O33199_MYCTO |
| AC: | O33199 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83331 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.160 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.220 | 617.625 |
| % Hydrophobic | % Polar |
|---|---|
| 37.70 | 62.30 |
| According to VolSite | |
| HET Code: | APR |
|---|---|
| Formula: | C15H21N5O14P2 |
| Molecular weight: | 557.300 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 32.18 % |
| Polar Surface area: | 316.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 26.5132 | 21.2342 | 4.60533 |
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 |
| C1' | CG2 | ILE- 19 | 4.06 | 0 | Hydrophobic |
| C3D | CB | ALA- 45 | 4.25 | 0 | Hydrophobic |
| C4D | CB | ALA- 45 | 4.09 | 0 | Hydrophobic |
| O1B | NH1 | ARG- 64 | 3.28 | 167.7 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 64 | 2.96 | 161.31 | H-Bond (Protein Donor) |
| O2B | CZ | ARG- 64 | 3.69 | 0 | Ionic (Protein Cationic) |
| C5D | CB | ALA- 76 | 4.07 | 0 | Hydrophobic |
| O2A | N | LEU- 78 | 2.87 | 166.49 | H-Bond (Protein Donor) |
| C5D | CD2 | LEU- 78 | 4.34 | 0 | Hydrophobic |
| C3D | CD2 | LEU- 78 | 4.16 | 0 | Hydrophobic |
| O3D | OE2 | GLU- 120 | 2.62 | 152.77 | H-Bond (Ligand Donor) |
| C1D | CD1 | ILE- 168 | 4.27 | 0 | Hydrophobic |
| C4D | CD1 | ILE- 168 | 4.03 | 0 | Hydrophobic |
