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
2001-01-09
| Name: | 3-hydroxy-3-methylglutaryl-coenzyme A reductase |
|---|---|
| ID: | HMDH_HUMAN |
| AC: | P04035 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.34 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 78 % |
| B | 22 % |
| B-Factor: | 62.861 |
|---|---|
| Number of residues: | 18 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.665 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 61.70 | 38.30 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 39.62 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -5.60511 | -1.43804 | -19.9216 |
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 |
| C3' | CZ | TYR- 479 | 4 | 0 | Hydrophobic |
| C2' | CE2 | TYR- 479 | 3.65 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 479 | 3.78 | 0 | Aromatic Face/Face |
| C1' | CB | ASN- 567 | 4.38 | 0 | Hydrophobic |
| N3 | ND2 | ASN- 567 | 3.09 | 137.28 | H-Bond (Protein Donor) |
| C5' | CD | ARG- 568 | 4.23 | 0 | Hydrophobic |
| C4' | CB | ARG- 568 | 3.89 | 0 | Hydrophobic |
| C1' | CB | ARG- 568 | 3.91 | 0 | Hydrophobic |
| O2B | NZ | LYS- 722 | 3.14 | 155.32 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 722 | 3.14 | 0 | Ionic (Protein Cationic) |
