sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-11-28
| Name: | NADH-cytochrome b5 reductase 3 |
|---|---|
| ID: | NB5R3_PIG |
| AC: | P83686 |
| Organism: | Sus scrofa |
| Reign: | Eukaryota |
| TaxID: | 9823 |
| EC Number: | 1.6.2.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 23.262 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.304 | 492.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.95 | 52.05 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 62.67 % |
| 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 |
|---|---|---|
| -16.0947 | -3.26255 | -6.30006 |
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 |
| O2A | NE | ARG- 63 | 3.18 | 129.04 | H-Bond (Protein Donor) |
| O2A | NH2 | ARG- 63 | 2.75 | 141.57 | H-Bond (Protein Donor) |
| O1P | NE | ARG- 63 | 3 | 127.58 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 63 | 3.36 | 0 | Ionic (Protein Cationic) |
| O1P | CZ | ARG- 63 | 3.71 | 0 | Ionic (Protein Cationic) |
| C3' | CD | ARG- 63 | 4.03 | 0 | Hydrophobic |
| C6 | CB | PRO- 64 | 3.66 | 0 | Hydrophobic |
| C7M | CB | PRO- 64 | 3.89 | 0 | Hydrophobic |
| C8M | CG | PRO- 64 | 3.64 | 0 | Hydrophobic |
| C8 | CG | PRO- 64 | 3.21 | 0 | Hydrophobic |
| O2' | O | PRO- 64 | 2.66 | 171.71 | H-Bond (Ligand Donor) |
| O4' | OH | TYR- 65 | 2.74 | 144.28 | H-Bond (Protein Donor) |
| C2' | CE1 | TYR- 65 | 3.61 | 0 | Hydrophobic |
| O4 | N | THR- 66 | 2.78 | 163.64 | H-Bond (Protein Donor) |
| N5 | OG1 | THR- 66 | 3.12 | 153.11 | H-Bond (Protein Donor) |
| N3 | O | VAL- 80 | 2.92 | 171.96 | H-Bond (Ligand Donor) |
| O2 | N | LYS- 82 | 3.15 | 162.03 | H-Bond (Protein Donor) |
| C3B | CD2 | TYR- 84 | 4.16 | 0 | Hydrophobic |
| C2B | CE1 | TYR- 84 | 4.24 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 84 | 3.62 | 0 | Hydrophobic |
| N6A | O | PHE- 85 | 2.85 | 132.96 | H-Bond (Ligand Donor) |
| C1B | CD1 | PHE- 92 | 3.65 | 0 | Hydrophobic |
| O1A | N | LYS- 97 | 2.8 | 162.19 | H-Bond (Protein Donor) |
| O3P | N | LYS- 97 | 3.44 | 130.52 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 97 | 3.99 | 0 | Ionic (Protein Cationic) |
| O1P | N | MET- 98 | 2.73 | 159.74 | H-Bond (Protein Donor) |
| O2P | N | SER- 99 | 2.86 | 160.48 | H-Bond (Protein Donor) |
| O2P | OG | SER- 99 | 2.86 | 150.64 | H-Bond (Protein Donor) |
| C7M | C3N | NAD- 302 | 4.22 | 0 | Hydrophobic |
| C1' | C2D | NAD- 302 | 3.81 | 0 | Hydrophobic |
| C9 | C2D | NAD- 302 | 4.44 | 0 | Hydrophobic |
| O4 | O | HOH- 433 | 2.72 | 179.97 | H-Bond (Protein Donor) |
