sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.490 Å
X-ray
2012-12-18
| Name: | 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase |
|---|---|
| ID: | ACMSD_HUMAN |
| AC: | Q8TDX5 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 4.1.1.45 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 96 % |
| C | 4 % |
| B-Factor: | 23.051 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.420 | 813.375 |
| % Hydrophobic | % Polar |
|---|---|
| 52.28 | 47.72 |
| According to VolSite | |
| HET Code: | PDC |
|---|---|
| Formula: | C7H3NO4 |
| Molecular weight: | 165.103 g/mol |
| DrugBank ID: | DB04267 |
| Buried Surface Area: | 69.79 % |
| Polar Surface area: | 93.15 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 5.70025 | -22.1692 | 54.5286 |
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 |
| N1 | NH1 | ARG- 47 | 2.92 | 160.55 | H-Bond (Protein Donor) |
| O3 | NH2 | ARG- 47 | 3.45 | 130.62 | H-Bond (Protein Donor) |
| C3 | CB | PRO- 77 | 3.55 | 0 | Hydrophobic |
| C4 | CG | PRO- 77 | 3.4 | 0 | Hydrophobic |
| O2 | N | VAL- 78 | 3.22 | 167.46 | H-Bond (Protein Donor) |
| DuAr | ZN | ZN- 401 | 3.57 | 96.8 | Pi/Cation |
