sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.910 Å
X-ray
2008-07-29
| 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: | 24.729 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.589 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 43.24 | 56.76 |
| According to VolSite | |
| HET Code: | O8M |
|---|---|
| Formula: | C14H22N7O4 |
| Molecular weight: | 352.369 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.68 % |
| Polar Surface area: | 166.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -17.4059 | -6.22836 | 5.49404 |
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 |
| C4' | CE2 | PHE- 7 | 4.29 | 0 | Hydrophobic |
| C2' | CG | PHE- 7 | 4.04 | 0 | Hydrophobic |
| C3' | CD2 | PHE- 7 | 3.78 | 0 | Hydrophobic |
| N3 | N | GLU- 67 | 3.3 | 155.4 | H-Bond (Protein Donor) |
| N7 | O | GLU- 67 | 3.3 | 154.21 | H-Bond (Ligand Donor) |
| C1' | CB | PHE- 223 | 4.18 | 0 | Hydrophobic |
| C8 | CB | PHE- 223 | 3.99 | 0 | Hydrophobic |
| C4' | CB | THR- 245 | 4.49 | 0 | Hydrophobic |
| C3' | CG2 | THR- 245 | 3.83 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 247 | 3.01 | 140.55 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 247 | 2.85 | 145.51 | H-Bond (Ligand Donor) |
