sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.410 Å
X-ray
2006-07-11
| Name: | tRNA-specific 2-thiouridylase MnmA |
|---|---|
| ID: | MNMA_STRPN |
| AC: | Q97T38 |
| Organism: | Streptococcus pneumoniae serotype 4 |
| Reign: | Bacteria |
| TaxID: | 170187 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 57.602 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.149 | 1356.750 |
| % Hydrophobic | % Polar |
|---|---|
| 37.06 | 62.94 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 64.48 % |
| Polar Surface area: | 189.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 30.0592 | 32.1761 | 10.8875 |
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 |
| O2' | O | GLY- 12 | 2.64 | 143.21 | H-Bond (Ligand Donor) |
| C2' | CB | SER- 14 | 4.31 | 0 | Hydrophobic |
| C2' | CB | SER- 19 | 3.88 | 0 | Hydrophobic |
| N6 | O | MET- 38 | 2.93 | 152.46 | H-Bond (Ligand Donor) |
| N1 | N | MET- 38 | 2.82 | 168.19 | H-Bond (Protein Donor) |
| O | ND2 | ASN- 104 | 2.76 | 165.23 | H-Bond (Protein Donor) |
| OXT | NZ | LYS- 108 | 2.88 | 177.53 | H-Bond (Protein Donor) |
| OXT | NZ | LYS- 108 | 2.88 | 0 | Ionic (Protein Cationic) |
| C1' | CD | LYS- 108 | 3.97 | 0 | Hydrophobic |
| C4' | CB | THR- 126 | 3.89 | 0 | Hydrophobic |
| C1' | CB | THR- 126 | 4.27 | 0 | Hydrophobic |
| O3' | N | GLY- 127 | 3.12 | 127.07 | H-Bond (Protein Donor) |
| O2' | N | GLY- 127 | 3.13 | 160.33 | H-Bond (Protein Donor) |
