sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2012-06-27
| Name: | DNA (cytosine-5)-methyltransferase 1 |
|---|---|
| ID: | CMT1_MAIZE |
| AC: | Q9AXT8 |
| Organism: | Zea mays |
| Reign: | Eukaryota |
| TaxID: | 4577 |
| EC Number: | 2.1.1.37 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 73.329 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.464 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 66.12 % |
| 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 |
|---|---|---|
| 0.0815 | -10.0059 | -23.7969 |
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 | TYR- 347 | 3.13 | 143.71 | H-Bond (Ligand Donor) |
| CG | CB | TYR- 347 | 4.45 | 0 | Hydrophobic |
| C1' | CB | TYR- 347 | 4.41 | 0 | Hydrophobic |
| C5' | CB | TYR- 347 | 3.89 | 0 | Hydrophobic |
| O | O | GLY- 349 | 2.63 | 148.9 | H-Bond (Ligand Donor) |
| O | N | GLY- 352 | 3.02 | 165.57 | H-Bond (Protein Donor) |
| O2' | OD2 | ASP- 375 | 2.78 | 143.94 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 375 | 3.28 | 155.08 | H-Bond (Ligand Donor) |
| C2' | CE2 | PHE- 376 | 3.76 | 0 | Hydrophobic |
| N1 | N | ALA- 398 | 3.09 | 162.45 | H-Bond (Protein Donor) |
| CB | CB | ASN- 851 | 4.16 | 0 | Hydrophobic |
| SD | CB | ASN- 851 | 3.96 | 0 | Hydrophobic |
| OXT | N | VAL- 853 | 2.85 | 159.76 | H-Bond (Protein Donor) |
