sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 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 | 30 % |
| A | 70 % |
| B-Factor: | 29.368 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.539 | 388.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.22 | 54.78 |
| According to VolSite | |
| HET Code: | A8M |
|---|---|
| Formula: | C15H27N7O3 |
| Molecular weight: | 353.420 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.67 % |
| Polar Surface area: | 151.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -67.8074 | -1.78644 | 5.55332 |
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 | 4.39 | 0 | Hydrophobic |
| C4' | CE2 | PHE- 7 | 4.43 | 0 | Hydrophobic |
| C2' | CG | PHE- 7 | 4.13 | 0 | Hydrophobic |
| C3' | CD2 | PHE- 7 | 3.84 | 0 | Hydrophobic |
| N1 | OE1 | GLU- 11 | 3.31 | 0 | Ionic (Ligand Cationic) |
| N3 | OG | SER- 66 | 3.14 | 163 | H-Bond (Protein Donor) |
| N3 | N | GLU- 67 | 3.09 | 157.17 | H-Bond (Protein Donor) |
| N7 | O | GLU- 67 | 3.42 | 141.38 | H-Bond (Ligand Donor) |
| C4 | CB | CYS- 82 | 4.39 | 0 | Hydrophobic |
| C1' | CB | PHE- 223 | 4.2 | 0 | Hydrophobic |
| C8 | CB | PHE- 223 | 4.16 | 0 | Hydrophobic |
| C4 | CB | HIS- 243 | 4.01 | 0 | Hydrophobic |
| C3' | CG2 | THR- 245 | 3.86 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 247 | 3.05 | 154.06 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 247 | 2.87 | 141.92 | H-Bond (Ligand Donor) |
