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
2012-08-29
| Name: | Cryptochrome-1 |
|---|---|
| ID: | CRY1_DROME |
| AC: | O77059 |
| Organism: | Drosophila melanogaster |
| Reign: | Eukaryota |
| TaxID: | 7227 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 21.030 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.718 | 1768.500 |
| % Hydrophobic | % Polar |
|---|---|
| 42.94 | 57.06 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 73.85 % |
| Polar Surface area: | 381.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 7 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -1.12434 | 46.5825 | 7.86626 |
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 | OG | SER- 265 | 2.85 | 160.14 | H-Bond (Protein Donor) |
| C3B | CB | SER- 267 | 4.31 | 0 | Hydrophobic |
| C5' | CB | SER- 267 | 3.74 | 0 | Hydrophobic |
| C4B | CD1 | LEU- 270 | 3.99 | 0 | Hydrophobic |
| O2A | NE2 | GLN- 311 | 3.05 | 164.28 | H-Bond (Protein Donor) |
| C1B | CB | GLN- 311 | 4.27 | 0 | Hydrophobic |
| C5B | CB | GLN- 311 | 3.8 | 0 | Hydrophobic |
| C4B | CD2 | LEU- 312 | 4.04 | 0 | Hydrophobic |
| C1B | CB | ARG- 315 | 4.29 | 0 | Hydrophobic |
| C5' | CZ2 | TRP- 375 | 4.07 | 0 | Hydrophobic |
| C2' | CB | HIS- 378 | 4.36 | 0 | Hydrophobic |
| C4' | CB | HIS- 378 | 4.41 | 0 | Hydrophobic |
| O2' | ND1 | HIS- 378 | 2.68 | 164.81 | H-Bond (Ligand Donor) |
| N5 | NH1 | ARG- 381 | 3.46 | 130.76 | H-Bond (Protein Donor) |
| C6 | CD | ARG- 381 | 4.2 | 0 | Hydrophobic |
| C9A | CD | ARG- 381 | 3.87 | 0 | Hydrophobic |
| C8 | CB | ARG- 381 | 3.76 | 0 | Hydrophobic |
| C7M | CB | ALA- 385 | 4.08 | 0 | Hydrophobic |
| C7M | CE2 | PHE- 404 | 3.73 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 412 | 3.16 | 138.86 | H-Bond (Ligand Donor) |
| O4 | N | ASP- 412 | 3.02 | 125.78 | H-Bond (Protein Donor) |
| C6 | SG | CYS- 416 | 3.97 | 0 | Hydrophobic |
| N6A | OD1 | ASN- 419 | 3.14 | 146.25 | H-Bond (Ligand Donor) |
| N1A | ND2 | ASN- 419 | 3.17 | 171.49 | H-Bond (Protein Donor) |
| C7M | CB | ASN- 419 | 4.25 | 0 | Hydrophobic |
| C8 | CB | ASN- 419 | 3.4 | 0 | Hydrophobic |
| C7M | CE2 | TRP- 420 | 3.84 | 0 | Hydrophobic |
| C8M | CG2 | VAL- 423 | 4.21 | 0 | Hydrophobic |
| C8M | CE1 | PHE- 534 | 4.49 | 0 | Hydrophobic |
| O1P | MG | MG- 601 | 2.38 | 0 | Metal Acceptor |
