sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2010-10-01
| Name: | RuvB-like 2 |
|---|---|
| ID: | RUVB2_HUMAN |
| AC: | Q9Y230 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.6.4.12 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 3 % |
| D | 97 % |
| B-Factor: | 95.653 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.602 | 1923.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.58 | 58.42 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 71.65 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 26.4921 | 84.9921 | 25.5012 |
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 |
| O3' | O | ALA- 39 | 2.8 | 159.03 | H-Bond (Ligand Donor) |
| O2' | ND1 | HIS- 40 | 2.78 | 167.59 | H-Bond (Ligand Donor) |
| N3 | NE2 | HIS- 42 | 2.9 | 151.98 | H-Bond (Protein Donor) |
| N6 | O | VAL- 62 | 2.62 | 123.84 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 62 | 2.9 | 164.04 | H-Bond (Protein Donor) |
| O3B | N | GLY- 95 | 2.93 | 165.95 | H-Bond (Protein Donor) |
| O1B | N | THR- 96 | 2.92 | 143.27 | H-Bond (Protein Donor) |
| O3A | N | GLY- 97 | 3.25 | 138.46 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 98 | 2.89 | 157.04 | H-Bond (Protein Donor) |
| O1B | N | LYS- 98 | 3.07 | 167.29 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 98 | 2.89 | 0 | Ionic (Protein Cationic) |
| O2B | N | THR- 99 | 2.85 | 165.77 | H-Bond (Protein Donor) |
| O2B | OG1 | THR- 99 | 2.72 | 172.25 | H-Bond (Protein Donor) |
| O2A | N | ALA- 100 | 2.98 | 150.3 | H-Bond (Protein Donor) |
| C2' | CB | ALA- 100 | 4.08 | 0 | Hydrophobic |
| N6 | OH | TYR- 277 | 2.81 | 147.26 | H-Bond (Ligand Donor) |
| C1' | CG2 | ILE- 285 | 3.69 | 0 | Hydrophobic |
| C5' | CD2 | LEU- 314 | 3.83 | 0 | Hydrophobic |
| C4' | CD1 | ILE- 318 | 3.78 | 0 | Hydrophobic |
