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
2002-05-17
| Name: | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial |
|---|---|
| ID: | HCDH_HUMAN |
| AC: | Q16836 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.35 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 32.437 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.530 | 1049.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.73 | 47.27 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 47.61 % |
| Polar Surface area: | 343.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 44.3235 | 53.7556 | 79.7451 |
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 |
| O2N | N | MET- 26 | 3.07 | 153.43 | H-Bond (Protein Donor) |
| C5D | CB | MET- 26 | 3.73 | 0 | Hydrophobic |
| C4D | CG | MET- 26 | 4.46 | 0 | Hydrophobic |
| C3N | CG | MET- 26 | 4.1 | 0 | Hydrophobic |
| C4N | SD | MET- 26 | 4.25 | 0 | Hydrophobic |
| C5N | CE | MET- 26 | 4.35 | 0 | Hydrophobic |
| O3B | OD2 | ASP- 45 | 2.83 | 151.25 | H-Bond (Ligand Donor) |
| O3B | OD1 | ASP- 45 | 3.4 | 129.9 | H-Bond (Ligand Donor) |
| O2B | OD1 | ASP- 45 | 2.68 | 164.07 | H-Bond (Ligand Donor) |
| O2B | NE2 | GLN- 46 | 2.95 | 147.95 | H-Bond (Protein Donor) |
| C5D | CB | ALA- 107 | 3.8 | 0 | Hydrophobic |
| C1B | CG2 | ILE- 108 | 4.15 | 0 | Hydrophobic |
| O3D | O | ILE- 108 | 2.68 | 147.83 | H-Bond (Ligand Donor) |
| O3D | NZ | LYS- 115 | 3.36 | 158.17 | H-Bond (Protein Donor) |
| C5N | CB | SER- 137 | 4.35 | 0 | Hydrophobic |
| C3N | CG2 | THR- 257 | 4.47 | 0 | Hydrophobic |
| O2N | O | HOH- 841 | 2.93 | 160.21 | H-Bond (Protein Donor) |
