sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2012-06-21
| Name: | 5-methylcytosine rRNA methyltransferase NSUN4 |
|---|---|
| ID: | NSUN4_HUMAN |
| AC: | Q96CB9 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 34.065 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.996 | 1171.125 |
| % Hydrophobic | % Polar |
|---|---|
| 39.48 | 60.52 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 69.22 % |
| 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 |
|---|---|---|
| 121.55 | 85.4747 | 48.272 |
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 |
| N | O | CYS- 181 | 3.04 | 153.96 | H-Bond (Ligand Donor) |
| C1' | CB | CYS- 181 | 4.29 | 0 | Hydrophobic |
| C4' | CB | CYS- 181 | 3.86 | 0 | Hydrophobic |
| O | N | GLY- 185 | 3.14 | 133.48 | H-Bond (Protein Donor) |
| O | N | GLY- 186 | 2.93 | 146.82 | H-Bond (Protein Donor) |
| OXT | NZ | LYS- 187 | 3.17 | 168.38 | H-Bond (Protein Donor) |
| OXT | N | LYS- 187 | 3.22 | 150.22 | H-Bond (Protein Donor) |
| OXT | NZ | LYS- 187 | 3.17 | 0 | Ionic (Protein Cationic) |
| O3' | OD1 | ASP- 204 | 2.74 | 170.35 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 204 | 3.48 | 135.43 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 204 | 2.67 | 157.9 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 205 | 3.34 | 165.52 | H-Bond (Protein Donor) |
| C3' | CD | ARG- 209 | 4.22 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 237 | 2.64 | 150.34 | H-Bond (Ligand Donor) |
| N1 | N | GLY- 238 | 2.85 | 157.93 | H-Bond (Protein Donor) |
| N | OD2 | ASP- 255 | 2.89 | 162.61 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 255 | 2.89 | 0 | Ionic (Ligand Cationic) |
| C2' | CB | PRO- 257 | 4.49 | 0 | Hydrophobic |
| C5' | CB | PRO- 257 | 3.99 | 0 | Hydrophobic |
