sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2006-08-09
| Name: | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding |
|---|---|
| ID: | B2J0D8_NOSP7 |
| AC: | B2J0D8 |
| Organism: | Nostoc punctiforme |
| Reign: | Bacteria |
| TaxID: | 63737 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 74 % |
| B | 26 % |
| B-Factor: | 31.825 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.031 | 658.125 |
| % Hydrophobic | % Polar |
|---|---|
| 62.56 | 37.44 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 73.65 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 26.2726 | 36.4319 | 16.8249 |
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 |
| C7M | CD1 | TYR- 23 | 3.56 | 0 | Hydrophobic |
| C2' | CB | TYR- 38 | 4.22 | 0 | Hydrophobic |
| C3' | CD2 | TYR- 38 | 3.96 | 0 | Hydrophobic |
| O2' | O | PRO- 39 | 2.84 | 169.83 | H-Bond (Ligand Donor) |
| C7 | CB | PRO- 39 | 4.02 | 0 | Hydrophobic |
| C8M | CG | PRO- 39 | 3.62 | 0 | Hydrophobic |
| C8 | CG | PRO- 39 | 3.62 | 0 | Hydrophobic |
| C2' | SD | MET- 40 | 4.23 | 0 | Hydrophobic |
| O4 | N | SER- 41 | 3.3 | 159.03 | H-Bond (Protein Donor) |
| N3 | O | PHE- 55 | 2.77 | 165.5 | H-Bond (Ligand Donor) |
| O2 | OG1 | THR- 56 | 3.35 | 162.8 | H-Bond (Protein Donor) |
| O2P | N | HIS- 61 | 3.23 | 158.68 | H-Bond (Protein Donor) |
| O4' | NZ | LYS- 62 | 2.65 | 169.22 | H-Bond (Protein Donor) |
| O1P | N | LYS- 62 | 2.84 | 157.95 | H-Bond (Protein Donor) |
| O1P | NZ | LYS- 62 | 2.62 | 165.74 | H-Bond (Protein Donor) |
| O1P | NZ | LYS- 62 | 2.62 | 0 | Ionic (Protein Cationic) |
| C7M | CE2 | TYR- 84 | 3.87 | 0 | Hydrophobic |
| C8M | CD2 | TYR- 84 | 4.08 | 0 | Hydrophobic |
| C7M | CZ2 | TRP- 111 | 3.95 | 0 | Hydrophobic |
| C6 | CZ2 | TRP- 111 | 3.24 | 0 | Hydrophobic |
| C8M | CB | TRP- 134 | 3.68 | 0 | Hydrophobic |
| C3' | CZ2 | TRP- 134 | 4.42 | 0 | Hydrophobic |
| O3' | NE1 | TRP- 134 | 3.14 | 142.86 | H-Bond (Protein Donor) |
| C8M | CA | SER- 139 | 4.3 | 0 | Hydrophobic |
| C1' | CD1 | PHE- 140 | 3.63 | 0 | Hydrophobic |
| C4' | CZ | PHE- 140 | 3.63 | 0 | Hydrophobic |
| O3' | O | PHE- 140 | 2.7 | 151.3 | H-Bond (Ligand Donor) |
