sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2014-05-14
| Name: | Actin, alpha skeletal muscle |
|---|---|
| ID: | ACTS_RABIT |
| AC: | P68135 |
| Organism: | Oryctolagus cuniculus |
| Reign: | Eukaryota |
| TaxID: | 9986 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 32.818 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 1.217 | 1073.250 |
| % Hydrophobic | % Polar |
|---|---|
| 52.83 | 47.17 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.02 % |
| 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 |
|---|---|---|
| 2.55733 | -18.1741 | 135.989 |
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 |
| O3B | N | SER- 14 | 3.33 | 120.44 | H-Bond (Protein Donor) |
| O3B | OG | SER- 14 | 3.13 | 150.56 | H-Bond (Protein Donor) |
| O2B | N | GLY- 15 | 2.79 | 141.56 | H-Bond (Protein Donor) |
| O2B | N | LEU- 16 | 2.84 | 147.35 | H-Bond (Protein Donor) |
| C5' | CD1 | LEU- 16 | 3.97 | 0 | Hydrophobic |
| O1B | NZ | LYS- 18 | 2.76 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 18 | 3.46 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 18 | 3.21 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 18 | 3.21 | 160.38 | H-Bond (Protein Donor) |
| O3B | N | ASP- 157 | 2.92 | 164.56 | H-Bond (Protein Donor) |
| O3A | N | ASP- 157 | 3.07 | 128.38 | H-Bond (Protein Donor) |
| C4' | CB | ASP- 157 | 4.25 | 0 | Hydrophobic |
| O2' | NZ | LYS- 213 | 2.9 | 138.94 | H-Bond (Protein Donor) |
| O2' | OE2 | GLU- 214 | 2.74 | 143.27 | H-Bond (Ligand Donor) |
| C2' | CG | GLU- 214 | 4.34 | 0 | Hydrophobic |
| O1A | N | GLY- 302 | 2.7 | 164.78 | H-Bond (Protein Donor) |
| O5' | N | GLY- 302 | 3.37 | 127.9 | H-Bond (Protein Donor) |
| O1B | CA | CA- 402 | 2.36 | 0 | Metal Acceptor |
| N3 | O | HOH- 509 | 3.15 | 161.02 | H-Bond (Protein Donor) |
