sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2010-12-02
| Name: | DNA (cytosine-5)-methyltransferase 1 |
|---|---|
| ID: | DNMT1_MOUSE |
| AC: | P13864 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 2.1.1.37 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.747 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.378 | 553.500 |
| % Hydrophobic | % Polar |
|---|---|
| 40.24 | 59.76 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 70.99 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -15.9158 | 2.00396 | 3.51827 |
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 |
| OXT | O | HOH- 3 | 2.89 | 162.07 | H-Bond (Protein Donor) |
| N | O | HOH- 7 | 2.99 | 163.59 | H-Bond (Ligand Donor) |
| C1' | CB | PHE- 1148 | 4.29 | 0 | Hydrophobic |
| C4' | CB | PHE- 1148 | 3.77 | 0 | Hydrophobic |
| OXT | N | GLY- 1152 | 3.4 | 140.61 | H-Bond (Protein Donor) |
| OXT | N | GLY- 1153 | 3.03 | 141.96 | H-Bond (Protein Donor) |
| O | N | LEU- 1154 | 2.83 | 129.24 | H-Bond (Protein Donor) |
| O3' | OE1 | GLU- 1171 | 2.94 | 155.87 | H-Bond (Ligand Donor) |
| N3 | N | MET- 1172 | 3.24 | 153.04 | H-Bond (Protein Donor) |
| N6 | OD2 | ASP- 1193 | 3.04 | 168.11 | H-Bond (Ligand Donor) |
| N1 | N | CYS- 1194 | 3.03 | 164.15 | H-Bond (Protein Donor) |
| C1' | CG | PRO- 1228 | 4.48 | 0 | Hydrophobic |
| C5' | CG | PRO- 1228 | 3.95 | 0 | Hydrophobic |
| SD | CB | ASN- 1580 | 3.76 | 0 | Hydrophobic |
| O | N | VAL- 1582 | 2.85 | 173.89 | H-Bond (Protein Donor) |
