sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.390 Å
X-ray
2012-07-19
| Name: | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial |
|---|---|
| ID: | NDI1_YEAST |
| AC: | P32340 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 1.6.5.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 36.624 |
|---|---|
| Number of residues: | 59 |
| Including | |
| Standard Amino Acids: | 54 |
| Non Standard Amino Acids: | 4 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.504 | 1981.125 |
| % Hydrophobic | % Polar |
|---|---|
| 44.97 | 55.03 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 68.99 % |
| 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 |
|---|---|---|
| 28.5204 | 36.9344 | -35.0046 |
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 |
| O3B | N | SER- 61 | 2.88 | 146.47 | H-Bond (Protein Donor) |
| O2A | N | TRP- 63 | 3.13 | 162.87 | H-Bond (Protein Donor) |
| C4' | CB | TRP- 63 | 4.27 | 0 | Hydrophobic |
| O1P | N | GLY- 64 | 2.79 | 162.4 | H-Bond (Protein Donor) |
| O2' | OG1 | THR- 91 | 2.79 | 161.72 | H-Bond (Protein Donor) |
| C9 | CB | THR- 91 | 3.82 | 0 | Hydrophobic |
| C7M | CB | LEU- 94 | 4.15 | 0 | Hydrophobic |
| C7M | CG | PRO- 95 | 4.03 | 0 | Hydrophobic |
| N6A | O | ALA- 129 | 2.97 | 170.15 | H-Bond (Ligand Donor) |
| N1A | N | ALA- 129 | 3.03 | 149.1 | H-Bond (Protein Donor) |
| C7M | CG | LEU- 195 | 4.48 | 0 | Hydrophobic |
| C8M | CG | LYS- 196 | 4.07 | 0 | Hydrophobic |
| C7M | CG2 | THR- 239 | 3.56 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 383 | 3.07 | 148.17 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 383 | 3.19 | 145.01 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 383 | 4.37 | 0 | Hydrophobic |
| O2P | N | ASP- 383 | 2.7 | 146.35 | H-Bond (Protein Donor) |
| N1 | N | ALA- 393 | 3.05 | 178.31 | H-Bond (Protein Donor) |
| C2' | CB | ALA- 393 | 3.82 | 0 | Hydrophobic |
| C4' | CB | ALA- 393 | 4.44 | 0 | Hydrophobic |
| O2 | N | GLN- 394 | 3.26 | 158.78 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 396 | 4.01 | 0 | Hydrophobic |
| O2P | MG | MG- 608 | 2.79 | 0 | Metal Acceptor |
| O1P | MG | MG- 609 | 2.64 | 0 | Metal Acceptor |
