sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.070 Å
X-ray
2011-06-27
| Name: | FAD-dependent catabolic D-arginine dehydrogenase DauA |
|---|---|
| ID: | DAUA_PSEAE |
| AC: | Q9HXE3 |
| Organism: | Pseudomonas aeruginosa |
| Reign: | Bacteria |
| TaxID: | 208964 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 7.675 |
|---|---|
| Number of residues: | 80 |
| Including | |
| Standard Amino Acids: | 73 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 7 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.904 | 276.750 |
| % Hydrophobic | % Polar |
|---|---|
| 53.66 | 46.34 |
| According to VolSite | |
| HET Code: | FNK |
|---|---|
| Formula: | C32H41N9O16P2 |
| Molecular weight: | 869.666 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 80.45 % |
| Polar Surface area: | 389.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 8 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 1.8692 | -15.4336 | -30.1281 |
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 |
| C4' | CG2 | ILE- 1013 | 4.23 | 0 | Hydrophobic |
| O1P | N | ALA- 1014 | 2.96 | 165.82 | H-Bond (Protein Donor) |
| O2B | OE2 | GLU- 1032 | 2.68 | 171.03 | H-Bond (Ligand Donor) |
| O3B | OE1 | GLU- 1032 | 2.71 | 177.14 | H-Bond (Ligand Donor) |
| O2B | NH2 | ARG- 1033 | 3 | 120.31 | H-Bond (Protein Donor) |
| N3A | N | ARG- 1033 | 3.13 | 144.86 | H-Bond (Protein Donor) |
| C3B | CB | HIS- 1040 | 4.18 | 0 | Hydrophobic |
| O2' | O | SER- 1041 | 3.05 | 125.8 | H-Bond (Ligand Donor) |
| O2A | N | SER- 1041 | 3.02 | 156.85 | H-Bond (Protein Donor) |
| C5' | CB | SER- 1041 | 3.94 | 0 | Hydrophobic |
| O1A | N | THR- 1042 | 2.9 | 142.76 | H-Bond (Protein Donor) |
| O1A | OG1 | THR- 1042 | 2.64 | 159.44 | H-Bond (Protein Donor) |
| O4' | OG1 | THR- 1042 | 3.14 | 162.72 | H-Bond (Ligand Donor) |
| C8M | CB | ARG- 1044 | 4.26 | 0 | Hydrophobic |
| C6 | CB | SER- 1045 | 4.35 | 0 | Hydrophobic |
| C2' | CB | SER- 1045 | 4.21 | 0 | Hydrophobic |
| C9A | CB | SER- 1045 | 3.63 | 0 | Hydrophobic |
| C6 | CB | ALA- 1046 | 4.14 | 0 | Hydrophobic |
| CB | CB | ALA- 1046 | 4.36 | 0 | Hydrophobic |
| CD2 | CB | ALA- 1046 | 3.75 | 0 | Hydrophobic |
| N3 | O | HIS- 1048 | 3 | 156.53 | H-Bond (Ligand Donor) |
| O4 | N | HIS- 1048 | 2.87 | 147.78 | H-Bond (Protein Donor) |
| CB | CE2 | TYR- 1053 | 4.17 | 0 | Hydrophobic |
| CG | CZ | TYR- 1053 | 4.29 | 0 | Hydrophobic |
| CD1 | CE2 | TYR- 1053 | 3.65 | 0 | Hydrophobic |
| N1A | N | ALA- 1171 | 2.94 | 166.1 | H-Bond (Protein Donor) |
| N6A | O | ALA- 1171 | 3.2 | 166.85 | H-Bond (Ligand Donor) |
| C2B | CE3 | TRP- 1202 | 4.39 | 0 | Hydrophobic |
| O | NH1 | ARG- 1222 | 3.05 | 148.59 | H-Bond (Protein Donor) |
| C7M | CG | ARG- 1222 | 3.72 | 0 | Hydrophobic |
| C8M | CB | ARG- 1222 | 4.41 | 0 | Hydrophobic |
| C7 | CD | ARG- 1222 | 3.99 | 0 | Hydrophobic |
| C7M | CB | ALA- 1224 | 4.35 | 0 | Hydrophobic |
| CD2 | CE | MET- 1240 | 3.26 | 0 | Hydrophobic |
| CD2 | CE2 | TYR- 1249 | 3.45 | 0 | Hydrophobic |
| C9 | CG | ARG- 1305 | 3.57 | 0 | Hydrophobic |
| C1' | CG | ARG- 1305 | 4.17 | 0 | Hydrophobic |
| C8M | CG | ARG- 1305 | 4.32 | 0 | Hydrophobic |
| C9A | CD | ARG- 1305 | 4.01 | 0 | Hydrophobic |
| C8 | CD | ARG- 1305 | 3.88 | 0 | Hydrophobic |
| C5' | CB | GLN- 1330 | 3.94 | 0 | Hydrophobic |
| O3' | O | GLY- 1331 | 2.85 | 169.67 | H-Bond (Ligand Donor) |
| O3' | N | GLY- 1334 | 2.91 | 135.76 | H-Bond (Protein Donor) |
| O2 | N | ILE- 1335 | 2.88 | 121.24 | H-Bond (Protein Donor) |
| C2' | CG1 | ILE- 1335 | 4.37 | 0 | Hydrophobic |
| C4' | CD1 | ILE- 1335 | 4.34 | 0 | Hydrophobic |
| O2 | N | GLN- 1336 | 2.84 | 165.58 | H-Bond (Protein Donor) |
| O1P | O | HOH- 2011 | 2.76 | 173.81 | H-Bond (Protein Donor) |
| O2P | O | HOH- 2017 | 2.92 | 145.77 | H-Bond (Protein Donor) |
| O3B | O | HOH- 2022 | 2.87 | 179.97 | H-Bond (Protein Donor) |
| O2A | O | HOH- 2027 | 2.72 | 135.66 | H-Bond (Protein Donor) |
