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
2012-03-12
| Name: | Histone-lysine N-methyltransferase SETD7 |
|---|---|
| ID: | SETD7_HUMAN |
| AC: | Q8WTS6 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1.43 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 25.495 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.108 | 1019.250 |
| % Hydrophobic | % Polar |
|---|---|
| 40.40 | 59.60 |
| According to VolSite | |
| HET Code: | 0N6 |
|---|---|
| Formula: | C23H27N4O3S |
| Molecular weight: | 439.550 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.24 % |
| Polar Surface area: | 115.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -42.2115 | -0.196226 | 27.5992 |
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 |
| C14 | CE1 | TYR- 245 | 4.44 | 0 | Hydrophobic |
| C15 | CZ | TYR- 245 | 4.23 | 0 | Hydrophobic |
| N1 | ND1 | HIS- 252 | 2.81 | 164.41 | H-Bond (Ligand Donor) |
| C6 | CG1 | VAL- 255 | 4.41 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 256 | 2.78 | 146.78 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 256 | 2.78 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 256 | 3.74 | 0 | Ionic (Ligand Cationic) |
| C19 | CB | ASN- 263 | 3.95 | 0 | Hydrophobic |
| C15 | CB | LEU- 267 | 4.4 | 0 | Hydrophobic |
| O1 | N | SER- 268 | 2.79 | 168.4 | H-Bond (Protein Donor) |
| C8 | CB | SER- 268 | 3.74 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 274 | 4.33 | 0 | Hydrophobic |
| C14 | CZ | TYR- 305 | 4.34 | 0 | Hydrophobic |
| C14 | CZ | TYR- 335 | 3.7 | 0 | Hydrophobic |
| N2 | O | GLY- 336 | 2.68 | 120.18 | H-Bond (Ligand Donor) |
| O2 | N | GLY- 336 | 2.78 | 173.64 | H-Bond (Protein Donor) |
| C11 | CE1 | TYR- 337 | 3.34 | 0 | Hydrophobic |
