sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.910 Å
X-ray
2015-02-17
| Name: | NADPH--cytochrome P450 reductase |
|---|---|
| ID: | NCPR_RAT |
| AC: | P00388 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 11 % |
| B | 89 % |
| B-Factor: | 29.365 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.399 | 708.750 |
| % Hydrophobic | % Polar |
|---|---|
| 38.57 | 61.43 |
| According to VolSite | |
| HET Code: | 2AM |
|---|---|
| Formula: | C10H12N5O7P |
| Molecular weight: | 345.205 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.7 % |
| Polar Surface area: | 201.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -42.9233 | 8.60109 | 34.8969 |
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' | CB | PRO- 533 | 4.23 | 0 | Hydrophobic |
| C3' | CG | ARG- 567 | 4.46 | 0 | Hydrophobic |
| O3P | OG | SER- 596 | 2.73 | 148.59 | H-Bond (Protein Donor) |
| O2' | OG | SER- 596 | 2.87 | 132.79 | H-Bond (Protein Donor) |
| O3' | OG | SER- 596 | 2.79 | 154.82 | H-Bond (Ligand Donor) |
| C2' | CB | SER- 596 | 4.4 | 0 | Hydrophobic |
| O2P | CZ | ARG- 597 | 3.85 | 0 | Ionic (Protein Cationic) |
| O3P | CZ | ARG- 597 | 3.59 | 0 | Ionic (Protein Cationic) |
| O2P | NH2 | ARG- 597 | 3 | 158.7 | H-Bond (Protein Donor) |
| O3P | NE | ARG- 597 | 2.77 | 171.13 | H-Bond (Protein Donor) |
| O1P | NZ | LYS- 602 | 3.31 | 0 | Ionic (Protein Cationic) |
| O3P | NZ | LYS- 602 | 2.71 | 0 | Ionic (Protein Cationic) |
| O3P | NZ | LYS- 602 | 2.71 | 151.45 | H-Bond (Protein Donor) |
| O1P | OH | TYR- 604 | 2.67 | 154.05 | H-Bond (Protein Donor) |
| DuAr | DuAr | TYR- 604 | 3.78 | 0 | Aromatic Face/Face |
| C1' | CE1 | TYR- 604 | 3.62 | 0 | Hydrophobic |
| N1 | NE2 | GLN- 606 | 3.07 | 158.3 | H-Bond (Protein Donor) |
| N6 | OD2 | ASP- 639 | 3.03 | 162.44 | H-Bond (Ligand Donor) |
