sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2012-03-28
| Name: | Phototropin-2 |
|---|---|
| ID: | PHOT2_ARATH |
| AC: | P93025 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.170 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.581 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 53.06 | 46.94 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 72.57 % |
| 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 |
|---|---|---|
| -1.01813 | 6.97758 | 41.9107 |
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 |
| C6 | CG2 | VAL- 392 | 3.67 | 0 | Hydrophobic |
| C7M | CB | SER- 394 | 3.95 | 0 | Hydrophobic |
| C8M | CB | SER- 394 | 4.12 | 0 | Hydrophobic |
| O2' | OD1 | ASN- 425 | 2.73 | 150.66 | H-Bond (Ligand Donor) |
| C6 | CB | CYS- 426 | 4.22 | 0 | Hydrophobic |
| C9A | CB | CYS- 426 | 3.74 | 0 | Hydrophobic |
| C2' | CB | ARG- 427 | 4.11 | 0 | Hydrophobic |
| O1P | CZ | ARG- 427 | 3.66 | 0 | Ionic (Protein Cationic) |
| O2P | CZ | ARG- 427 | 3.73 | 0 | Ionic (Protein Cationic) |
| O1P | NH2 | ARG- 427 | 2.9 | 149.43 | H-Bond (Protein Donor) |
| O2P | NE | ARG- 427 | 2.83 | 170.53 | H-Bond (Protein Donor) |
| N1 | NE2 | GLN- 430 | 3.38 | 143.87 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 430 | 2.98 | 158.16 | H-Bond (Protein Donor) |
| O4' | NE2 | GLN- 430 | 2.85 | 171.19 | H-Bond (Protein Donor) |
| C5' | CG1 | VAL- 439 | 3.82 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 442 | 3.81 | 0 | Hydrophobic |
| C4' | CG2 | ILE- 442 | 4.25 | 0 | Hydrophobic |
| C5' | CB | ARG- 443 | 3.83 | 0 | Hydrophobic |
| O3P | NH1 | ARG- 443 | 2.94 | 153.56 | H-Bond (Protein Donor) |
| C3' | CD1 | ILE- 446 | 4.47 | 0 | Hydrophobic |
| C8M | CD1 | ILE- 446 | 3.89 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 458 | 3.15 | 149.26 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 458 | 2.71 | 164.69 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 468 | 3.04 | 123.97 | H-Bond (Protein Donor) |
| C7 | CD1 | LEU- 472 | 4.06 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 472 | 3.85 | 0 | Hydrophobic |
| C7M | CB | PHE- 485 | 3.73 | 0 | Hydrophobic |
| C8M | CB | PHE- 485 | 3.71 | 0 | Hydrophobic |
| O4 | NE2 | GLN- 489 | 3.09 | 145.02 | H-Bond (Protein Donor) |
| N5 | NE2 | GLN- 489 | 3.39 | 138.8 | H-Bond (Protein Donor) |
| O2' | O | HOH- 1107 | 3.39 | 158.36 | H-Bond (Protein Donor) |
| O2' | O | HOH- 1111 | 3.18 | 132.83 | H-Bond (Protein Donor) |
