sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2012-12-07
| Name: | NAD-dependent histone deacetylase SIR2 |
|---|---|
| ID: | SIR2_YEAST |
| AC: | P06700 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 3.5.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| C | 3 % |
| B-Factor: | 60.781 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.885 | 904.500 |
| % Hydrophobic | % Polar |
|---|---|
| 48.13 | 51.87 |
| According to VolSite | |
| HET Code: | APR |
|---|---|
| Formula: | C15H21N5O14P2 |
| Molecular weight: | 557.300 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.95 % |
| Polar Surface area: | 316.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 96.2763 | 63.4854 | 69.4989 |
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 |
| O2B | N | ALA- 263 | 2.5 | 155.47 | H-Bond (Protein Donor) |
| N6 | OG1 | THR- 267 | 3.11 | 162.58 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 273 | 4.16 | 0 | Hydrophobic |
| C2D | CE1 | PHE- 274 | 3.41 | 0 | Hydrophobic |
| O1A | N | ARG- 275 | 2.66 | 162.58 | H-Bond (Protein Donor) |
| O3D | ND1 | HIS- 364 | 3.14 | 140.35 | H-Bond (Protein Donor) |
| C1D | CZ | PHE- 445 | 3.78 | 0 | Hydrophobic |
| O1B | OG1 | THR- 472 | 3.07 | 161.64 | H-Bond (Protein Donor) |
| O5' | N | SER- 473 | 3.5 | 132.45 | H-Bond (Protein Donor) |
| O1B | N | SER- 473 | 3.13 | 146.83 | H-Bond (Protein Donor) |
| C1D | CG2 | VAL- 476 | 4.33 | 0 | Hydrophobic |
| C4D | CG2 | VAL- 476 | 3.66 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 496 | 3.08 | 176.88 | H-Bond (Protein Donor) |
| N3 | N | ARG- 497 | 3.06 | 138.61 | H-Bond (Protein Donor) |
| N1 | N | CYS- 513 | 3.03 | 148.53 | H-Bond (Protein Donor) |
| C1D | CE | MET- 747 | 3.76 | 0 | Hydrophobic |
