sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.240 Å
X-ray
2009-04-10
| Name: | S-adenosylmethionine decarboxylase proenzyme |
|---|---|
| ID: | DCAM_HUMAN |
| AC: | P17707 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 4.1.1.50 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 29 % |
| A | 71 % |
| B-Factor: | 30.774 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.567 | 378.000 |
| % Hydrophobic | % Polar |
|---|---|
| 44.64 | 55.36 |
| According to VolSite | |
| HET Code: | M2T |
|---|---|
| Formula: | C12H19N5O3S |
| Molecular weight: | 313.376 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.68 % |
| Polar Surface area: | 123.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -16.3581 | -5.41595 | 5.62105 |
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 |
| C2' | CG | PHE- 7 | 3.75 | 0 | Hydrophobic |
| C3' | CD2 | PHE- 7 | 3.68 | 0 | Hydrophobic |
| C5' | CE2 | PHE- 7 | 3.57 | 0 | Hydrophobic |
| N1 | N | GLU- 67 | 3.17 | 152.19 | H-Bond (Protein Donor) |
| N6 | OXT | GLU- 67 | 3.33 | 174.16 | H-Bond (Ligand Donor) |
| CG | SG | CYS- 82 | 3.59 | 0 | Hydrophobic |
| C1' | CB | PHE- 223 | 4.48 | 0 | Hydrophobic |
| CE | CE1 | PHE- 223 | 3.8 | 0 | Hydrophobic |
| CE | CB | SER- 229 | 4.31 | 0 | Hydrophobic |
| CG | CB | HIS- 243 | 4.47 | 0 | Hydrophobic |
| C4' | CB | THR- 245 | 4.3 | 0 | Hydrophobic |
| C3' | CG2 | THR- 245 | 3.7 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 247 | 3.09 | 150.93 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 247 | 3.36 | 142.71 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 247 | 2.66 | 121.13 | H-Bond (Ligand Donor) |
