sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.460 Å
X-ray
2015-02-17
| Name: | Acyl-CoA synthetase (NDP forming) |
|---|---|
| ID: | B1L3C9_KORCO |
| AC: | B1L3C9 |
| Organism: | Korarchaeum cryptofilum |
| Reign: | Archaea |
| TaxID: | 374847 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 93 % |
| C | 7 % |
| B-Factor: | 59.544 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.289 | 1333.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.03 | 57.97 |
| According to VolSite | |
| HET Code: | COA |
|---|---|
| Formula: | C21H32N7O16P3S |
| Molecular weight: | 763.502 g/mol |
| DrugBank ID: | DB01992 |
| Buried Surface Area: | 50.31 % |
| Polar Surface area: | 426.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 39.4013 | 11.6824 | 85.3483 |
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 |
| O7A | OG | SER- 19 | 2.52 | 155.52 | H-Bond (Protein Donor) |
| O7A | NZ | LYS- 24 | 2.64 | 171.85 | H-Bond (Protein Donor) |
| O2A | NZ | LYS- 24 | 2.66 | 155.54 | H-Bond (Protein Donor) |
| O7A | NZ | LYS- 24 | 2.64 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 24 | 2.66 | 0 | Ionic (Protein Cationic) |
| C5B | CD | LYS- 24 | 4.22 | 0 | Hydrophobic |
| CEP | CD1 | ILE- 25 | 3.79 | 0 | Hydrophobic |
| C6P | CD1 | ILE- 25 | 4.17 | 0 | Hydrophobic |
| O8A | ND2 | ASN- 46 | 2.89 | 170.17 | H-Bond (Protein Donor) |
| C1B | CG | PRO- 47 | 4.21 | 0 | Hydrophobic |
| CCP | CG | PRO- 76 | 4.29 | 0 | Hydrophobic |
| C6P | CG2 | ILE- 98 | 4.5 | 0 | Hydrophobic |
| CDP | CB | THR- 99 | 4.28 | 0 | Hydrophobic |
| O9P | N | SER- 100 | 2.85 | 162.49 | H-Bond (Protein Donor) |
| C6P | CB | SER- 100 | 4.31 | 0 | Hydrophobic |
| C2P | CB | PHE- 131 | 4.09 | 0 | Hydrophobic |
| C2P | CZ | PHE- 144 | 4.02 | 0 | Hydrophobic |
