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
2010-10-15
| Name: | D-galactonate dehydratase family member ManD |
|---|---|
| ID: | DMGD_CHRSD |
| AC: | Q1QT89 |
| Organism: | Chromohalobacter salexigens |
| Reign: | Bacteria |
| TaxID: | 290398 |
| EC Number: | 4.2.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 8 % |
| D | 92 % |
| B-Factor: | 17.985 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.159 | 769.500 |
| % Hydrophobic | % Polar |
|---|---|
| 35.09 | 64.91 |
| According to VolSite | |
| HET Code: | KDG |
|---|---|
| Formula: | C6H9O6 |
| Molecular weight: | 177.132 g/mol |
| DrugBank ID: | DB03489 |
| Buried Surface Area: | 81.14 % |
| Polar Surface area: | 117.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -52.7647 | -22.7569 | 78.7602 |
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 |
| O1B | ND2 | ASN- 39 | 3.02 | 169.97 | H-Bond (Protein Donor) |
| C1 | CE2 | TYR- 77 | 3.79 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 77 | 4.37 | 0 | Hydrophobic |
| C1 | CH2 | TRP- 78 | 4.23 | 0 | Hydrophobic |
| O3 | NE2 | HIS- 215 | 2.9 | 146.84 | H-Bond (Protein Donor) |
| O5 | NE2 | HIS- 215 | 2.92 | 122.83 | H-Bond (Protein Donor) |
| C2 | CB | PRO- 317 | 4.48 | 0 | Hydrophobic |
| C4 | CB | PRO- 317 | 4.33 | 0 | Hydrophobic |
| O1B | OD2 | ASP- 319 | 2.91 | 134.46 | H-Bond (Ligand Donor) |
| O2 | OD1 | ASP- 319 | 2.73 | 161.44 | H-Bond (Ligand Donor) |
| C1 | CD1 | LEU- 392 | 3.97 | 0 | Hydrophobic |
| C1 | CZ3 | TRP- 405 | 4.42 | 0 | Hydrophobic |
| O5 | MG | MG- 406 | 2.38 | 0 | Metal Acceptor |
| O6A | MG | MG- 406 | 2.26 | 0 | Metal Acceptor |
