sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.740 Å
X-ray
2008-01-02
| 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: | 26.941 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.752 | 543.375 |
| % Hydrophobic | % Polar |
|---|---|
| 49.69 | 50.31 |
| According to VolSite | |
| HET Code: | TDC |
|---|---|
| Formula: | C22H21N2O7 |
| Molecular weight: | 425.411 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.49 % |
| Polar Surface area: | 168.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -24.9435 | 8.70587 | -21.8961 |
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 |
| O3 | NE2 | HIS- 64 | 2.71 | 163.55 | H-Bond (Protein Donor) |
| N4 | OD1 | ASN- 82 | 2.78 | 152.6 | H-Bond (Ligand Donor) |
| O3 | ND2 | ASN- 82 | 2.91 | 159.45 | H-Bond (Protein Donor) |
| C9 | CD | ARG- 104 | 4.16 | 0 | Hydrophobic |
| C61 | CG | PRO- 105 | 3.81 | 0 | Hydrophobic |
| C1A | CG | PRO- 105 | 3.64 | 0 | Hydrophobic |
| C62 | CB | VAL- 113 | 3.72 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 113 | 3.82 | 0 | Hydrophobic |
| O3 | NE2 | GLN- 116 | 3.22 | 146.6 | H-Bond (Protein Donor) |
| O21 | NE2 | GLN- 116 | 3.37 | 145.23 | H-Bond (Protein Donor) |
| C62 | CG | LEU- 117 | 4.35 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 131 | 3.92 | 0 | Hydrophobic |
| C5 | CG2 | ILE- 134 | 3.91 | 0 | Hydrophobic |
| C62 | CG2 | ILE- 134 | 3.91 | 0 | Hydrophobic |
| O12 | MG | MG- 1207 | 2.02 | 0 | Metal Acceptor |
| O11 | MG | MG- 1207 | 1.98 | 0 | Metal Acceptor |
