sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.010 Å
X-ray
2013-06-18
| Name: | L-malyl-CoA/beta-methylmalyl-CoA lyase |
|---|---|
| ID: | MCAL_RHOS4 |
| AC: | Q3J5L6 |
| Organism: | Rhodobacter sphaeroides |
| Reign: | Bacteria |
| TaxID: | 272943 |
| EC Number: | 4.1.3.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 22 % |
| F | 78 % |
| B-Factor: | 15.911 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.182 | 668.250 |
| % Hydrophobic | % Polar |
|---|---|
| 62.63 | 37.37 |
| According to VolSite | |
| HET Code: | COA |
|---|---|
| Formula: | C21H32N7O16P3S |
| Molecular weight: | 763.502 g/mol |
| DrugBank ID: | DB01992 |
| Buried Surface Area: | 47.94 % |
| 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 |
|---|---|---|
| 51.2217 | -56.994 | -14.5395 |
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 |
| N6A | O | PHE- 19 | 2.99 | 163.73 | H-Bond (Ligand Donor) |
| C2P | CD2 | PHE- 19 | 3.55 | 0 | Hydrophobic |
| C2B | CD2 | LEU- 27 | 4.27 | 0 | Hydrophobic |
| C1B | CD | LYS- 30 | 4.09 | 0 | Hydrophobic |
| C6P | CB | SER- 46 | 4.35 | 0 | Hydrophobic |
| S1P | CB | PRO- 223 | 4.19 | 0 | Hydrophobic |
| CEP | CE2 | PHE- 227 | 4.1 | 0 | Hydrophobic |
| C2P | CZ3 | TRP- 249 | 3.79 | 0 | Hydrophobic |
| N8P | O | ILE- 251 | 2.73 | 143.32 | H-Bond (Ligand Donor) |
| S1P | CG2 | ILE- 251 | 3.53 | 0 | Hydrophobic |
| O2A | NE2 | HIS- 252 | 2.96 | 156.61 | H-Bond (Protein Donor) |
| C1B | CG | PRO- 253 | 4 | 0 | Hydrophobic |
| C4B | CG | PRO- 253 | 4.44 | 0 | Hydrophobic |
| CCP | CG2 | VAL- 292 | 3.96 | 0 | Hydrophobic |
| CDP | CG2 | VAL- 292 | 4.5 | 0 | Hydrophobic |
| CEP | CD1 | LEU- 297 | 4.25 | 0 | Hydrophobic |
| S1P | CD2 | LEU- 297 | 3.97 | 0 | Hydrophobic |
