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
2004-05-27
| Name: | Ribosomal RNA small subunit methyltransferase H |
|---|---|
| ID: | RSMH_THET8 |
| AC: | Q5SJD8 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.075 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.044 | 1252.125 |
| % Hydrophobic | % Polar |
|---|---|
| 39.08 | 60.92 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 77.67 % |
| 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 |
|---|---|---|
| 53.2753 | 82.3058 | 5.69441 |
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 | THR- 30 | 4.3 | 0 | Hydrophobic |
| C4' | CB | THR- 30 | 3.82 | 0 | Hydrophobic |
| OXT | N | GLY- 33 | 2.9 | 134.71 | H-Bond (Protein Donor) |
| OXT | N | GLY- 35 | 3.11 | 165.72 | H-Bond (Protein Donor) |
| N | ND1 | HIS- 36 | 2.86 | 134.67 | H-Bond (Ligand Donor) |
| O | N | HIS- 36 | 3.14 | 136.61 | H-Bond (Protein Donor) |
| O3' | OD1 | ASP- 51 | 3.38 | 132.68 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 51 | 2.72 | 168.74 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 51 | 2.59 | 162.97 | H-Bond (Ligand Donor) |
| N7 | NE2 | GLN- 52 | 3.4 | 137.25 | H-Bond (Protein Donor) |
| N3 | N | GLN- 52 | 3.19 | 139.38 | H-Bond (Protein Donor) |
| N6 | OD1 | ASN- 74 | 3.07 | 162.53 | H-Bond (Ligand Donor) |
| N1 | N | PHE- 75 | 2.79 | 162.71 | H-Bond (Protein Donor) |
| N | OD2 | ASP- 96 | 2.77 | 159.83 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 96 | 2.77 | 0 | Ionic (Ligand Cationic) |
| C3' | CB | SER- 100 | 3.74 | 0 | Hydrophobic |
| C2' | SD | MET- 123 | 4.33 | 0 | Hydrophobic |
| N | O | HOH- 3199 | 2.9 | 161.83 | H-Bond (Ligand Donor) |
