sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2014-07-14
| Name: | F420H(2)-dependent reductase Rv1155 |
|---|---|
| ID: | Y1155_MYCTU |
| AC: | O06553 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 1.4.3.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 67 % |
| B | 33 % |
| B-Factor: | 35.392 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.419 | 931.500 |
| % Hydrophobic | % Polar |
|---|---|
| 38.41 | 61.59 |
| According to VolSite | |
| HET Code: | F42 |
|---|---|
| Formula: | C29H32N5O18P |
| Molecular weight: | 769.561 g/mol |
| DrugBank ID: | DB03913 |
| Buried Surface Area: | 64.22 % |
| Polar Surface area: | 389.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 20 |
| H-Bond Donors: | 7 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 20 |
| X | Y | Z |
|---|---|---|
| 8.6952 | 18.7047 | 14.9114 |
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 |
| C7 | CD1 | ILE- 19 | 4.01 | 0 | Hydrophobic |
| O2' | O | ASN- 35 | 3.39 | 162.69 | H-Bond (Ligand Donor) |
| C7 | CB | ASN- 35 | 3.48 | 0 | Hydrophobic |
| O4 | N | GLN- 37 | 2.73 | 161.7 | H-Bond (Protein Donor) |
| N3 | O | SER- 50 | 2.77 | 127.71 | H-Bond (Ligand Donor) |
| C3' | CD | ARG- 55 | 4.27 | 0 | Hydrophobic |
| C5' | CD | ARG- 55 | 3.63 | 0 | Hydrophobic |
| C7 | CB | TRP- 77 | 4.33 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 77 | 3.51 | 0 | Aromatic Face/Face |
| O4' | OH | TYR- 79 | 3.05 | 159.25 | H-Bond (Ligand Donor) |
| C1' | CD2 | LEU- 142 | 4.32 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 142 | 3.68 | 0 | Hydrophobic |
| O4 | O | HOH- 411 | 2.58 | 179.97 | H-Bond (Protein Donor) |
