sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.890 Å
X-ray
2011-12-12
| Name: | Tetracycline repressor protein class D |
|---|---|
| ID: | TETR4_ECOLX |
| AC: | P0ACT4 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 562 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 34.948 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.711 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 39.41 | 60.59 |
| According to VolSite | |
| HET Code: | T1C |
|---|---|
| Formula: | C29H38N5O8 |
| Molecular weight: | 584.641 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 44.36 % |
| Polar Surface area: | 220.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 22.2502 | 38.7041 | 33.9077 |
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 |
| N4 | OD1 | ASN- 82 | 2.69 | 139.32 | H-Bond (Ligand Donor) |
| O3 | ND2 | ASN- 82 | 2.83 | 165.38 | H-Bond (Protein Donor) |
| C1A | CG | PRO- 105 | 3.95 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 113 | 4.3 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 113 | 4.07 | 0 | Hydrophobic |
| O3 | NE2 | GLN- 116 | 2.82 | 150.69 | H-Bond (Protein Donor) |
| O21 | NE2 | GLN- 116 | 3.4 | 130.01 | H-Bond (Protein Donor) |
| C71 | CD1 | LEU- 131 | 3.59 | 0 | Hydrophobic |
| C72 | CD1 | LEU- 131 | 4.11 | 0 | Hydrophobic |
| C71 | CG2 | ILE- 134 | 4 | 0 | Hydrophobic |
| C5 | CG2 | ILE- 134 | 4.17 | 0 | Hydrophobic |
| O12 | MG | MG- 1210 | 1.9 | 0 | Metal Acceptor |
| O11 | MG | MG- 1210 | 2.08 | 0 | Metal Acceptor |
