sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
1994-07-13
| Name: | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial |
|---|---|
| ID: | ACADM_PIG |
| AC: | P41367 |
| Organism: | Sus scrofa |
| Reign: | Eukaryota |
| TaxID: | 9823 |
| EC Number: | 1.3.8.7 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 2 % |
| B | 98 % |
| B-Factor: | 17.215 |
|---|---|
| Number of residues: | 53 |
| Including | |
| Standard Amino Acids: | 48 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.308 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 55.47 | 44.53 |
| According to VolSite | |
| HET Code: | CO8 |
|---|---|
| Formula: | C29H46N7O17P3S |
| Molecular weight: | 889.699 g/mol |
| DrugBank ID: | DB02910 |
| Buried Surface Area: | 52.46 % |
| Polar Surface area: | 429.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 26 |
| X | Y | Z |
|---|---|---|
| -1.09009 | -18.7484 | 0.457018 |
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 |
| C8' | CG2 | THR- 96 | 4.38 | 0 | Hydrophobic |
| C6' | CG2 | THR- 96 | 3.63 | 0 | Hydrophobic |
| C7' | CB | GLU- 99 | 3.47 | 0 | Hydrophobic |
| C6' | CB | ALA- 100 | 4.17 | 0 | Hydrophobic |
| C5' | CD2 | LEU- 103 | 3.34 | 0 | Hydrophobic |
| S1P | CE2 | TYR- 133 | 4.07 | 0 | Hydrophobic |
| N4P | O | GLY- 141 | 3.27 | 137.04 | H-Bond (Ligand Donor) |
| OAP | O | SER- 142 | 3.2 | 161.33 | H-Bond (Ligand Donor) |
| N8P | O | SER- 142 | 3.07 | 140.22 | H-Bond (Ligand Donor) |
| C6P | CG1 | VAL- 144 | 3.54 | 0 | Hydrophobic |
| C5' | CB | THR- 168 | 4.45 | 0 | Hydrophobic |
| C5B | CB | ALA- 190 | 4.03 | 0 | Hydrophobic |
| O8A | OG | SER- 191 | 2.87 | 141.75 | H-Bond (Protein Donor) |
| C4B | CB | SER- 191 | 4.29 | 0 | Hydrophobic |
| C1B | CE2 | PHE- 245 | 4.28 | 0 | Hydrophobic |
| C5B | CE2 | PHE- 245 | 3.56 | 0 | Hydrophobic |
| CEP | SD | MET- 249 | 4.32 | 0 | Hydrophobic |
| CAP | CE | MET- 249 | 4.36 | 0 | Hydrophobic |
| S1P | CE1 | PHE- 252 | 3.88 | 0 | Hydrophobic |
| C8' | CG2 | VAL- 259 | 4.1 | 0 | Hydrophobic |
| CDP | CZ | PHE- 284 | 4.33 | 0 | Hydrophobic |
| C8' | CZ | TYR- 375 | 4.22 | 0 | Hydrophobic |
| C4' | CD2 | TYR- 375 | 3.48 | 0 | Hydrophobic |
| S1P | CG | GLU- 376 | 4.44 | 0 | Hydrophobic |
| C2' | CG | GLU- 376 | 3.42 | 0 | Hydrophobic |
| O1' | N | GLU- 376 | 2.87 | 123.17 | H-Bond (Protein Donor) |
| CDP | CG2 | ILE- 381 | 4.41 | 0 | Hydrophobic |
| CEP | CG1 | ILE- 385 | 3.98 | 0 | Hydrophobic |
| C2P | C2' | FAD- 399 | 4.35 | 0 | Hydrophobic |
| O1' | O2' | FAD- 399 | 2.89 | 167.51 | H-Bond (Protein Donor) |
| O4A | O | HOH- 946 | 3.07 | 154.3 | H-Bond (Protein Donor) |
