sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2010-08-23
| 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 | 100 % |
| B-Factor: | 31.667 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.127 | 654.750 |
| % Hydrophobic | % Polar |
|---|---|
| 51.55 | 48.45 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 78.33 % |
| 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 |
|---|---|---|
| 5.48252 | 10.8529 | 17.3088 |
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 |
| O3P | OG | SER- 86 | 2.58 | 152.11 | H-Bond (Protein Donor) |
| O2P | N | GLN- 87 | 2.86 | 156.79 | H-Bond (Protein Donor) |
| O1P | N | THR- 88 | 3.38 | 128.36 | H-Bond (Protein Donor) |
| O2P | N | THR- 88 | 3.06 | 152.06 | H-Bond (Protein Donor) |
| O2P | OG1 | THR- 88 | 3.46 | 127.72 | H-Bond (Protein Donor) |
| O1P | OG1 | THR- 90 | 2.68 | 147.64 | H-Bond (Protein Donor) |
| O1P | N | THR- 90 | 2.71 | 153.82 | H-Bond (Protein Donor) |
| O3P | N | ALA- 91 | 2.68 | 167.73 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 138 | 3.98 | 0 | Hydrophobic |
| O2' | N | THR- 139 | 3.37 | 137.8 | H-Bond (Protein Donor) |
| O2' | O | THR- 139 | 2.74 | 162.58 | H-Bond (Ligand Donor) |
| C7M | CD2 | TYR- 140 | 4.12 | 0 | Hydrophobic |
| C8M | CE2 | TYR- 140 | 3.8 | 0 | Hydrophobic |
| C5' | CE1 | TYR- 140 | 4.26 | 0 | Hydrophobic |
| O2P | OH | TYR- 140 | 2.69 | 150.9 | H-Bond (Protein Donor) |
| C4' | CB | LEU- 173 | 3.68 | 0 | Hydrophobic |
| O2 | N | ASN- 175 | 2.91 | 152.49 | H-Bond (Protein Donor) |
| C1' | CB | ASN- 175 | 3.97 | 0 | Hydrophobic |
| C1' | CE2 | TYR- 178 | 4.09 | 0 | Hydrophobic |
| N3 | O | HIS- 180 | 3 | 162.54 | H-Bond (Ligand Donor) |
| O2 | N | ASN- 182 | 2.75 | 173.18 | H-Bond (Protein Donor) |
| C3' | CB | ASP- 208 | 4.23 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 208 | 3.25 | 139.04 | H-Bond (Ligand Donor) |
| C7M | CG2 | VAL- 676 | 3.39 | 0 | Hydrophobic |
| C7M | C8M | FAD- 752 | 4.03 | 0 | Hydrophobic |
