sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2007-03-30
| Name: | UDP-N-acetylglucosamine pyrophosphorylase |
|---|---|
| ID: | UAP1_CANAX |
| AC: | O74933 |
| Organism: | Candida albicans |
| Reign: | Eukaryota |
| TaxID: | 5476 |
| EC Number: | 2.7.7.23 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.632 |
|---|---|
| Number of residues: | 48 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.661 | 1012.500 |
| % Hydrophobic | % Polar |
|---|---|
| 32.67 | 67.33 |
| According to VolSite | |
| HET Code: | UD1 |
|---|---|
| Formula: | C17H25N3O17P2 |
| Molecular weight: | 605.338 g/mol |
| DrugBank ID: | DB03397 |
| Buried Surface Area: | 70.24 % |
| Polar Surface area: | 325.69 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: | 10 |
| X | Y | Z |
|---|---|---|
| 10.4037 | -1.62805 | 33.8579 |
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 |
| C1B | CB | MET- 109 | 3.83 | 0 | Hydrophobic |
| C4B | CB | MET- 109 | 4.49 | 0 | Hydrophobic |
| O2' | O | MET- 109 | 3.31 | 175.87 | H-Bond (Ligand Donor) |
| O2 | N | GLY- 111 | 2.87 | 143.99 | H-Bond (Protein Donor) |
| O2' | N | GLY- 112 | 3.19 | 143.51 | H-Bond (Protein Donor) |
| O1B | NH2 | ARG- 116 | 2.86 | 152.97 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 116 | 3.94 | 0 | Ionic (Protein Cationic) |
| N3 | OE1 | GLN- 199 | 2.67 | 164.04 | H-Bond (Ligand Donor) |
| O4 | NE2 | GLN- 199 | 2.93 | 143.87 | H-Bond (Protein Donor) |
| O7' | ND2 | ASN- 227 | 2.8 | 156.75 | H-Bond (Protein Donor) |
| O4B | ND2 | ASN- 227 | 3.31 | 154.42 | H-Bond (Protein Donor) |
| C1B | CB | ASN- 227 | 4.18 | 0 | Hydrophobic |
| C3B | SG | CYS- 255 | 3.41 | 0 | Hydrophobic |
| C3B | CG1 | VAL- 256 | 4.49 | 0 | Hydrophobic |
| O3B | N | VAL- 256 | 3.1 | 152.4 | H-Bond (Protein Donor) |
| C6' | CG1 | VAL- 293 | 4.18 | 0 | Hydrophobic |
| O3' | N | GLY- 294 | 3.35 | 130.93 | H-Bond (Protein Donor) |
| O4' | N | GLY- 294 | 2.7 | 148.7 | H-Bond (Protein Donor) |
| N2' | OE2 | GLU- 309 | 2.73 | 163.44 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 309 | 2.81 | 150.82 | H-Bond (Ligand Donor) |
| C3' | CE2 | TYR- 310 | 4.34 | 0 | Hydrophobic |
| O2B | OH | TYR- 310 | 2.64 | 177.01 | H-Bond (Protein Donor) |
| C4' | CB | ASN- 335 | 4.24 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 335 | 2.8 | 137.35 | H-Bond (Protein Donor) |
| O4' | O | ASN- 335 | 2.78 | 150.07 | H-Bond (Ligand Donor) |
| C1' | CG2 | VAL- 337 | 3.79 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 337 | 3.92 | 0 | Hydrophobic |
| C8' | CD1 | PHE- 393 | 3.5 | 0 | Hydrophobic |
| C8' | CE2 | PHE- 395 | 3.64 | 0 | Hydrophobic |
| C6' | CZ | PHE- 417 | 3.87 | 0 | Hydrophobic |
| O6' | NZ | LYS- 421 | 2.86 | 142.19 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 421 | 2.79 | 172.39 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 421 | 2.79 | 0 | Ionic (Protein Cationic) |
| O2A | O | HOH- 1370 | 3.37 | 179.96 | H-Bond (Protein Donor) |
| O1B | O | HOH- 1396 | 2.71 | 179.97 | H-Bond (Protein Donor) |
