sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.760 Å
X-ray
2006-11-21
| Name: | rRNA methyltransferase 2, mitochondrial |
|---|---|
| ID: | MRM2_HUMAN |
| AC: | Q9UI43 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 3 % |
| B | 97 % |
| B-Factor: | 32.169 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.113 | 867.375 |
| % Hydrophobic | % Polar |
|---|---|
| 38.13 | 61.87 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 72.23 % |
| 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 |
|---|---|---|
| 21.2838 | 23.8463 | 6.87263 |
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 |
| O | N | GLY- 34 | 2.91 | 158.15 | H-Bond (Protein Donor) |
| O | N | ALA- 35 | 2.92 | 150.19 | H-Bond (Protein Donor) |
| OXT | N | TRP- 36 | 2.93 | 142.5 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 62 | 2.82 | 171.38 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 62 | 3.2 | 128.6 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 62 | 2.53 | 165.53 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 63 | 3.36 | 154.71 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 79 | 2.99 | 152.77 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 80 | 2.9 | 162.69 | H-Bond (Protein Donor) |
| N | OD2 | ASP- 104 | 2.8 | 169.52 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 104 | 2.8 | 0 | Ionic (Ligand Cationic) |
| CG | CB | ASP- 104 | 4.14 | 0 | Hydrophobic |
