sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.080 Å
X-ray
2012-03-27
| Name: | UDP-glucose 6-dehydrogenase |
|---|---|
| ID: | UGDH_HUMAN |
| AC: | O60701 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.22 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 95 % |
| C | 5 % |
| B-Factor: | 31.111 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.579 | 965.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.96 | 58.04 |
| According to VolSite | |
| HET Code: | UPG |
|---|---|
| Formula: | C15H22N2O17P2 |
| Molecular weight: | 564.286 g/mol |
| DrugBank ID: | DB01861 |
| Buried Surface Area: | 75.08 % |
| Polar Surface area: | 316.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 7 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 55.2167 | 16.6911 | 49.0331 |
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 |
| C6' | CG | GLU- 161 | 4.29 | 0 | Hydrophobic |
| O4' | O | PHE- 162 | 3.41 | 163.09 | H-Bond (Ligand Donor) |
| C3' | CB | ALA- 164 | 4.31 | 0 | Hydrophobic |
| O2B | N | GLU- 165 | 2.98 | 172.14 | H-Bond (Protein Donor) |
| O4' | NZ | LYS- 220 | 3.1 | 147.8 | H-Bond (Protein Donor) |
| O6' | NZ | LYS- 220 | 3.42 | 120.24 | H-Bond (Protein Donor) |
| O6' | ND2 | ASN- 224 | 3.12 | 156.29 | H-Bond (Protein Donor) |
| C2' | CD1 | LEU- 227 | 4.14 | 0 | Hydrophobic |
| C1C | CD1 | ILE- 231 | 3.93 | 0 | Hydrophobic |
| O2' | NH2 | ARG- 260 | 3.28 | 123.38 | H-Bond (Protein Donor) |
| O2' | NH1 | ARG- 260 | 2.67 | 143.13 | H-Bond (Protein Donor) |
| O3' | NH2 | ARG- 260 | 2.71 | 157.97 | H-Bond (Protein Donor) |
| N3 | O | LYS- 267 | 3 | 176.5 | H-Bond (Ligand Donor) |
| O4 | N | LYS- 267 | 3.19 | 153.67 | H-Bond (Protein Donor) |
| O2 | OG | SER- 269 | 2.8 | 162.01 | H-Bond (Protein Donor) |
| C1C | CB | PHE- 272 | 3.86 | 0 | Hydrophobic |
| C4C | CB | PHE- 272 | 3.76 | 0 | Hydrophobic |
| O3C | N | GLY- 273 | 3.05 | 158.75 | H-Bond (Protein Donor) |
| C5' | CB | CYS- 276 | 4.45 | 0 | Hydrophobic |
| C6' | SG | CYS- 276 | 3.41 | 0 | Hydrophobic |
| C4C | CD2 | PHE- 277 | 4.3 | 0 | Hydrophobic |
| C5C | CE2 | PHE- 277 | 3.67 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 277 | 3.71 | 0 | Hydrophobic |
| O3C | O | PHE- 338 | 2.57 | 164.76 | H-Bond (Ligand Donor) |
| C5C | CE2 | PHE- 338 | 4.01 | 0 | Hydrophobic |
| C3C | CD2 | PHE- 338 | 3.65 | 0 | Hydrophobic |
| O1A | NZ | LYS- 339 | 2.69 | 168.15 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 339 | 2.69 | 0 | Ionic (Protein Cationic) |
| C3C | CB | LYS- 339 | 4 | 0 | Hydrophobic |
| O2C | NH1 | ARG- 442 | 2.65 | 143.13 | H-Bond (Protein Donor) |
| O2C | NH2 | ARG- 442 | 2.97 | 130.01 | H-Bond (Protein Donor) |
| O1B | O | HOH- 601 | 2.58 | 145.6 | H-Bond (Protein Donor) |
