sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.420 Å
X-ray
2011-05-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.300 | 6.410 | 6.410 | 0.110 | 6.520 | 2 |
| Name: | N-lysine methyltransferase SMYD2 |
|---|---|
| ID: | SMYD2_HUMAN |
| AC: | Q9NRG4 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 39.492 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.790 | 742.500 |
| % Hydrophobic | % Polar |
|---|---|
| 35.00 | 65.00 |
| According to VolSite | |
| HET Code: | NH5 |
|---|---|
| Formula: | C29H40Cl2N4O4 |
| Molecular weight: | 579.558 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.64 % |
| Polar Surface area: | 112.09 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -16.8743 | -58.6108 | 2.24085 |
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 |
| C34 | CB | THR- 105 | 4.04 | 0 | Hydrophobic |
| C36 | CD2 | LEU- 108 | 4.21 | 0 | Hydrophobic |
| CL39 | CD1 | LEU- 141 | 3.86 | 0 | Hydrophobic |
| CL39 | CD | LYS- 145 | 4.49 | 0 | Hydrophobic |
| C3 | CD | LYS- 145 | 3.96 | 0 | Hydrophobic |
| C4 | CG | LYS- 145 | 3.93 | 0 | Hydrophobic |
| CL38 | CB | LEU- 148 | 4.36 | 0 | Hydrophobic |
| CL38 | CG1 | ILE- 149 | 3.74 | 0 | Hydrophobic |
| CL39 | CD1 | ILE- 149 | 3.66 | 0 | Hydrophobic |
| CL39 | CB | ALA- 177 | 4.08 | 0 | Hydrophobic |
| C36 | CG1 | VAL- 179 | 4.11 | 0 | Hydrophobic |
| C11 | CB | ASN- 180 | 4.3 | 0 | Hydrophobic |
| C3 | CB | ASN- 180 | 3.6 | 0 | Hydrophobic |
| C27 | CE2 | PHE- 184 | 4.38 | 0 | Hydrophobic |
| C35 | CB | SER- 196 | 4.03 | 0 | Hydrophobic |
| C23 | CG2 | THR- 238 | 3.72 | 0 | Hydrophobic |
| C20 | CB | TYR- 240 | 4.29 | 0 | Hydrophobic |
| C1 | CB | SER- 257 | 4.41 | 0 | Hydrophobic |
| C7 | CB | SER- 257 | 4.17 | 0 | Hydrophobic |
| C19 | CZ | TYR- 258 | 4.3 | 0 | Hydrophobic |
| C27 | CE1 | TYR- 258 | 4.43 | 0 | Hydrophobic |
| N17 | O | HOH- 524 | 3.21 | 168.7 | H-Bond (Ligand Donor) |
