sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2012-05-04
| Name: | 5-methylthioadenosine/S-adenosylhomocysteine deaminase |
|---|---|
| ID: | Q7NZ90_CHRVO |
| AC: | Q7NZ90 |
| Organism: | Chromobacterium violaceum |
| Reign: | Bacteria |
| TaxID: | 243365 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.025 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.137 | 850.500 |
| % Hydrophobic | % Polar |
|---|---|
| 59.92 | 40.08 |
| According to VolSite | |
| HET Code: | MTA |
|---|---|
| Formula: | C11H15N5O3S |
| Molecular weight: | 297.333 g/mol |
| DrugBank ID: | DB02282 |
| Buried Surface Area: | 58.52 % |
| Polar Surface area: | 144.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 0.3939 | 20.0522 | 21.3815 |
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 |
| C3' | SD | MET- 75 | 4.48 | 0 | Hydrophobic |
| O2' | NE1 | TRP- 96 | 2.97 | 124.89 | H-Bond (Protein Donor) |
| DuAr | DuAr | TRP- 96 | 3.48 | 0 | Aromatic Face/Face |
| O2' | OE2 | GLU- 99 | 3.48 | 123.03 | H-Bond (Ligand Donor) |
| O2' | OE1 | GLU- 99 | 2.52 | 151.84 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 99 | 2.97 | 121.03 | H-Bond (Ligand Donor) |
| CS | CE | MET- 130 | 4.05 | 0 | Hydrophobic |
| C3' | CE1 | TYR- 131 | 4.15 | 0 | Hydrophobic |
| CS | CD1 | TYR- 131 | 4.43 | 0 | Hydrophobic |
| CS | CZ | PHE- 132 | 4.41 | 0 | Hydrophobic |
| C4' | CZ | PHE- 132 | 3.59 | 0 | Hydrophobic |
| C3' | CE1 | PHE- 132 | 4.22 | 0 | Hydrophobic |
| C1' | CZ | PHE- 132 | 4.5 | 0 | Hydrophobic |
| CS | CB | SER- 153 | 3.84 | 0 | Hydrophobic |
