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
2005-09-26
| Name: | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase |
|---|---|
| ID: | RHLG_PSEAE |
| AC: | Q9RPT1 |
| Organism: | Pseudomonas aeruginosa |
| Reign: | Bacteria |
| TaxID: | 208964 |
| EC Number: | 1.1.1.100 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 24.801 |
|---|---|
| Number of residues: | 51 |
| Including | |
| Standard Amino Acids: | 50 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.138 | 1059.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.54 | 54.46 |
| According to VolSite | |
| HET Code: | NAP |
|---|---|
| Formula: | C21H25N7O17P3 |
| Molecular weight: | 740.381 g/mol |
| DrugBank ID: | DB03461 |
| Buried Surface Area: | 74.3 % |
| Polar Surface area: | 405.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -14.8107 | 87.7172 | 8.25752 |
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 |
| O3B | O | GLY- 16 | 3.13 | 120.17 | H-Bond (Ligand Donor) |
| O3B | OG | SER- 18 | 2.69 | 150.39 | H-Bond (Protein Donor) |
| O3B | N | SER- 18 | 3.37 | 140.89 | H-Bond (Protein Donor) |
| O2A | NE | ARG- 19 | 2.8 | 141.72 | H-Bond (Protein Donor) |
| O5B | NE | ARG- 19 | 2.91 | 122.33 | H-Bond (Protein Donor) |
| O3X | NH1 | ARG- 19 | 3.3 | 122.14 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 19 | 3.92 | 0 | Ionic (Protein Cationic) |
| O1X | CZ | ARG- 19 | 3.13 | 0 | Ionic (Protein Cationic) |
| O3X | CZ | ARG- 19 | 3.82 | 0 | Ionic (Protein Cationic) |
| C5B | CG | ARG- 19 | 4.43 | 0 | Hydrophobic |
| C3B | CG | ARG- 19 | 3.98 | 0 | Hydrophobic |
| O2N | N | ILE- 21 | 3.34 | 165.99 | H-Bond (Protein Donor) |
| C5D | CB | ILE- 21 | 3.84 | 0 | Hydrophobic |
| C3N | CD1 | ILE- 21 | 3.95 | 0 | Hydrophobic |
| C2B | CB | ALA- 40 | 4.18 | 0 | Hydrophobic |
| O3X | NE | ARG- 41 | 3.16 | 145.18 | H-Bond (Protein Donor) |
| O3X | NH2 | ARG- 41 | 2.97 | 153.11 | H-Bond (Protein Donor) |
| O3X | CZ | ARG- 41 | 3.51 | 0 | Ionic (Protein Cationic) |
| O2X | N | ASP- 42 | 2.62 | 174.64 | H-Bond (Protein Donor) |
| N6A | OD2 | ASP- 65 | 3.27 | 130.19 | H-Bond (Ligand Donor) |
| N1A | N | LEU- 66 | 2.66 | 163.41 | H-Bond (Protein Donor) |
| O3D | O | ASN- 92 | 2.51 | 152.69 | H-Bond (Ligand Donor) |
| C1B | CB | ALA- 93 | 4.28 | 0 | Hydrophobic |
| C4D | CG2 | ILE- 146 | 3.9 | 0 | Hydrophobic |
| C5N | CB | SER- 148 | 3.35 | 0 | Hydrophobic |
| C2D | CZ | TYR- 162 | 4.5 | 0 | Hydrophobic |
| O2D | OH | TYR- 162 | 2.9 | 159.84 | H-Bond (Protein Donor) |
| O3D | NZ | LYS- 166 | 3.33 | 161.57 | H-Bond (Protein Donor) |
| O2D | NZ | LYS- 166 | 3.39 | 132.25 | H-Bond (Protein Donor) |
| C4N | CB | PRO- 192 | 3.99 | 0 | Hydrophobic |
| C5N | CG | PRO- 192 | 3.94 | 0 | Hydrophobic |
| O7N | N | PHE- 195 | 2.91 | 156 | H-Bond (Protein Donor) |
| N7N | O | PHE- 195 | 3.42 | 149.23 | H-Bond (Ligand Donor) |
| O1N | OG | SER- 197 | 3.44 | 156.23 | H-Bond (Protein Donor) |
| O3 | O | HOH- 1920 | 2.9 | 179.96 | H-Bond (Protein Donor) |
