sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2015-01-12
| Name: | Lmo1466 protein |
|---|---|
| ID: | Q8Y746_LISMO |
| AC: | Q8Y746 |
| Organism: | Listeria monocytogenes serovar 1/2a |
| Reign: | Bacteria |
| TaxID: | 169963 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 4 % |
| D | 96 % |
| B-Factor: | 24.351 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | FE FE |
| Ligandability | Volume (Å3) |
|---|---|
| 0.882 | 1586.250 |
| % Hydrophobic | % Polar |
|---|---|
| 38.72 | 61.28 |
| According to VolSite | |
| HET Code: | 2BA |
|---|---|
| Formula: | C20H22N10O12P2 |
| Molecular weight: | 656.396 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.68 % |
| Polar Surface area: | 334.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 20 |
| H-Bond Donors: | 4 |
| Rings: | 7 |
| Aromatic rings: | 4 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 45.8316 | -6.06355 | 3.62961 |
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 |
| O2P | NZ | LYS- 547 | 3.24 | 130.52 | H-Bond (Protein Donor) |
| O3'1 | NZ | LYS- 547 | 2.92 | 138.27 | H-Bond (Protein Donor) |
| O2'1 | NZ | LYS- 547 | 2.87 | 142.38 | H-Bond (Protein Donor) |
| C4'1 | CD1 | PHE- 554 | 4.32 | 0 | Hydrophobic |
| C1'1 | CD1 | PHE- 554 | 3.73 | 0 | Hydrophobic |
| C2'1 | CG1 | VAL- 555 | 4.15 | 0 | Hydrophobic |
| N31 | N | VAL- 555 | 3.26 | 132.85 | H-Bond (Protein Donor) |
| O2'1 | OE1 | GLU- 556 | 2.75 | 162.59 | H-Bond (Ligand Donor) |
| C1'1 | CD1 | ILE- 577 | 4.3 | 0 | Hydrophobic |
| C5'1 | CG2 | ILE- 577 | 3.69 | 0 | Hydrophobic |
| O2P1 | OH | TYR- 631 | 2.53 | 160.26 | H-Bond (Protein Donor) |
| C1' | CB | SER- 649 | 3.64 | 0 | Hydrophobic |
| C5' | CB | ALA- 652 | 3.72 | 0 | Hydrophobic |
| N61 | OE1 | GLU- 659 | 3.01 | 165.62 | H-Bond (Ligand Donor) |
| O1P | FE | FE- 801 | 2.18 | 0 | Metal Acceptor |
| O2P | FE | FE- 802 | 2.26 | 0 | Metal Acceptor |
