sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.510 Å
X-ray
2009-08-12
| Name: | UDP-galactopyranose mutase |
|---|---|
| ID: | GLF1_KLEPN |
| AC: | Q48485 |
| Organism: | Klebsiella pneumoniae |
| Reign: | Bacteria |
| TaxID: | 573 |
| EC Number: | 5.4.99.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 37.847 |
|---|---|
| Number of residues: | 61 |
| Including | |
| Standard Amino Acids: | 54 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 6 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.003 | 2767.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.27 | 55.73 |
| According to VolSite | |
| HET Code: | FDA |
|---|---|
| Formula: | C27H33N9O15P2 |
| Molecular weight: | 785.550 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.27 % |
| Polar Surface area: | 381.04 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 9 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 11.945 | -17.399 | 5.77249 |
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 |
| O1P | N | SER- 14 | 2.95 | 165.41 | H-Bond (Protein Donor) |
| O2P | OG | SER- 14 | 2.57 | 162.86 | H-Bond (Protein Donor) |
| O3B | OD2 | ASP- 33 | 2.65 | 158.86 | H-Bond (Ligand Donor) |
| O3B | OD1 | ASP- 33 | 3.43 | 129.44 | H-Bond (Ligand Donor) |
| O2B | OD1 | ASP- 33 | 3 | 158.17 | H-Bond (Ligand Donor) |
| N3A | N | GLN- 34 | 3.06 | 140.51 | H-Bond (Protein Donor) |
| O2A | N | ASN- 41 | 2.86 | 165.71 | H-Bond (Protein Donor) |
| O2' | NE2 | HIS- 60 | 2.7 | 173.73 | H-Bond (Protein Donor) |
| N3 | O | ILE- 61 | 2.85 | 157.47 | H-Bond (Ligand Donor) |
| O4 | N | ILE- 61 | 2.79 | 171.64 | H-Bond (Protein Donor) |
| N1A | N | PHE- 219 | 3.06 | 145.22 | H-Bond (Protein Donor) |
| N6A | OH | TYR- 232 | 3.34 | 125.53 | H-Bond (Ligand Donor) |
| C7M | CD1 | LEU- 252 | 3.79 | 0 | Hydrophobic |
| C7M | CD2 | TYR- 313 | 4 | 0 | Hydrophobic |
| C8M | CD2 | TYR- 313 | 3.54 | 0 | Hydrophobic |
| C7M | CZ | TYR- 314 | 3.78 | 0 | Hydrophobic |
| O1A | CZ | ARG- 343 | 3.92 | 0 | Ionic (Protein Cationic) |
| O1A | NH1 | ARG- 343 | 2.73 | 139.93 | H-Bond (Protein Donor) |
| C5' | CD | ARG- 343 | 3.79 | 0 | Hydrophobic |
| C5B | CD1 | LEU- 344 | 4.4 | 0 | Hydrophobic |
| C8M | CE1 | TYR- 349 | 4.49 | 0 | Hydrophobic |
| C1' | CZ | TYR- 349 | 4.13 | 0 | Hydrophobic |
| O3' | O | LEU- 350 | 2.55 | 174.94 | H-Bond (Ligand Donor) |
| N1 | N | MET- 352 | 3.29 | 131.45 | H-Bond (Protein Donor) |
| O2 | N | MET- 352 | 2.57 | 167.08 | H-Bond (Protein Donor) |
| C2' | CG | MET- 352 | 4.16 | 0 | Hydrophobic |
| O3' | OG1 | THR- 355 | 3.08 | 161.92 | H-Bond (Protein Donor) |
| C5' | CG2 | THR- 355 | 3.85 | 0 | Hydrophobic |
| O3B | O | HOH- 398 | 3.04 | 145.66 | H-Bond (Protein Donor) |
| O1P | O | HOH- 477 | 2.97 | 179.96 | H-Bond (Protein Donor) |
| O2P | O | HOH- 484 | 2.66 | 179.98 | H-Bond (Protein Donor) |
