sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.030 Å
X-ray
2006-07-06
| Name: | Dynactin subunit 1 |
|---|---|
| ID: | DCTN1_HUMAN |
| AC: | Q14203 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 77 % |
| B | 23 % |
| B-Factor: | 26.674 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.781 | 351.000 |
| % Hydrophobic | % Polar |
|---|---|
| 51.92 | 48.08 |
| According to VolSite | |
| HET Code: | GLU_GLU_TYR |
|---|---|
| Formula: | C19H23N3O9 |
| Molecular weight: | 437.401 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.99 % |
| Polar Surface area: | 226.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 13.5961 | 16.3622 | -1.98639 |
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 |
| CG | CD | LYS- 38 | 4.3 | 0 | Hydrophobic |
| CB | CE2 | PHE- 52 | 3.68 | 0 | Hydrophobic |
| CG | CD2 | PHE- 52 | 3.35 | 0 | Hydrophobic |
| CE1 | CB | PHE- 52 | 4.11 | 0 | Hydrophobic |
| CE2 | CB | ALA- 53 | 4.21 | 0 | Hydrophobic |
| CG | CH2 | TRP- 57 | 3.86 | 0 | Hydrophobic |
| O | NZ | LYS- 68 | 2.8 | 154.74 | H-Bond (Protein Donor) |
| CB | CD | LYS- 68 | 4.01 | 0 | Hydrophobic |
| O | ND2 | ASN- 69 | 2.74 | 151.99 | H-Bond (Protein Donor) |
| CD1 | CG1 | VAL- 73 | 4.02 | 0 | Hydrophobic |
| CB | CD1 | ILE- 87 | 4.4 | 0 | Hydrophobic |
| N | O | PHE- 88 | 3.06 | 153.92 | H-Bond (Ligand Donor) |
| CB | CB | PHE- 88 | 4.06 | 0 | Hydrophobic |
| OXT | N | PHE- 88 | 2.64 | 161.12 | H-Bond (Protein Donor) |
| CG | CG1 | VAL- 89 | 4.06 | 0 | Hydrophobic |
| OE2 | NE2 | GLN- 93 | 2.71 | 153.01 | H-Bond (Protein Donor) |
| O | O | HOH- 117 | 2.76 | 167.29 | H-Bond (Protein Donor) |
