sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
1996-04-11
| Name: | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial |
|---|---|
| ID: | ACADM_HUMAN |
| AC: | P11310 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.3.8.7 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 98 % |
| D | 2 % |
| B-Factor: | 13.440 |
|---|---|
| Number of residues: | 49 |
| Including | |
| Standard Amino Acids: | 48 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.069 | 641.250 |
| % Hydrophobic | % Polar |
|---|---|
| 64.21 | 35.79 |
| According to VolSite | |
| HET Code: | CO8 |
|---|---|
| Formula: | C29H46N7O17P3S |
| Molecular weight: | 889.699 g/mol |
| DrugBank ID: | DB02910 |
| Buried Surface Area: | 52.45 % |
| 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 |
|---|---|---|
| 138.917 | 66.2347 | 91.9741 |
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' | CG2 | THR- 96 | 4.21 | 0 | Hydrophobic |
| C6' | CG2 | THR- 96 | 4.21 | 0 | Hydrophobic |
| C8' | CG2 | THR- 96 | 3.97 | 0 | Hydrophobic |
| C6' | CB | GLU- 99 | 3.82 | 0 | Hydrophobic |
| C7' | CG | GLU- 99 | 3.43 | 0 | Hydrophobic |
| S1P | CD1 | LEU- 103 | 4.29 | 0 | Hydrophobic |
| C2' | CD1 | LEU- 103 | 3.94 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 103 | 3.42 | 0 | Hydrophobic |
| S1P | CD1 | TYR- 133 | 4.04 | 0 | Hydrophobic |
| OAP | O | SER- 142 | 2.81 | 158.37 | H-Bond (Ligand Donor) |
| N8P | O | SER- 142 | 2.9 | 160.8 | H-Bond (Ligand Donor) |
| CAP | CG2 | VAL- 144 | 3.86 | 0 | Hydrophobic |
| C6P | CG2 | VAL- 144 | 3.66 | 0 | Hydrophobic |
| OAP | N | VAL- 144 | 3.41 | 164.24 | H-Bond (Protein Donor) |
| C1B | CD2 | PHE- 245 | 4.13 | 0 | Hydrophobic |
| C5B | CE2 | PHE- 245 | 4.03 | 0 | Hydrophobic |
| C1B | CG | MET- 249 | 4.48 | 0 | Hydrophobic |
| CAP | CE | MET- 249 | 3.62 | 0 | Hydrophobic |
| C6P | CZ | PHE- 252 | 3.94 | 0 | Hydrophobic |
| C2P | CZ | PHE- 252 | 3.73 | 0 | Hydrophobic |
| S1P | CE1 | PHE- 252 | 3.97 | 0 | Hydrophobic |
| C7' | CG1 | VAL- 259 | 3.6 | 0 | Hydrophobic |
| CCP | CE2 | PHE- 284 | 4.29 | 0 | Hydrophobic |
| C2' | CG | TYR- 375 | 4.29 | 0 | Hydrophobic |
| C3' | CD2 | TYR- 375 | 3.54 | 0 | Hydrophobic |
| C4' | CE2 | TYR- 375 | 3.54 | 0 | Hydrophobic |
| C8' | CZ | TYR- 375 | 3.71 | 0 | Hydrophobic |
| O1' | N | GLY- 376 | 3.08 | 130.5 | H-Bond (Protein Donor) |
| CDP | CB | ILE- 381 | 4.02 | 0 | Hydrophobic |
| CDP | CD1 | ILE- 385 | 4.14 | 0 | Hydrophobic |
| CEP | CG1 | ILE- 385 | 4.44 | 0 | Hydrophobic |
| N7A | NH1 | ARG- 388 | 3.16 | 149.84 | H-Bond (Protein Donor) |
| O1' | O2' | FAD- 399 | 2.83 | 178.98 | H-Bond (Protein Donor) |
