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
2013-05-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.030 | 6.940 | 7.860 | 1.350 | 7.940 | 3 |
| Name: | Enoyl-[acyl-carrier-protein] reductase [NADH] |
|---|---|
| ID: | INHA_MYCTU |
| AC: | P9WGR1 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 1.3.1.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 94 % |
| E | 6 % |
| B-Factor: | 18.352 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.477 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.03 | 42.97 |
| According to VolSite | |
| HET Code: | VMY |
|---|---|
| Formula: | C18H16F2N6OS2 |
| Molecular weight: | 434.486 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.79 % |
| Polar Surface area: | 145.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 22.6076 | -5.3929 | 38.3974 |
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 |
| N3 | O | MET- 98 | 2.85 | 154.78 | H-Bond (Ligand Donor) |
| N2 | N | MET- 98 | 3.12 | 146.39 | H-Bond (Protein Donor) |
| S1 | SD | MET- 103 | 3.89 | 0 | Hydrophobic |
| C17 | CG | MET- 103 | 4.25 | 0 | Hydrophobic |
| C15 | CE | MET- 103 | 3.76 | 0 | Hydrophobic |
| C | CB | PHE- 149 | 3.7 | 0 | Hydrophobic |
| C16 | CB | ALA- 157 | 3.83 | 0 | Hydrophobic |
| F | CB | ALA- 157 | 4.35 | 0 | Hydrophobic |
| C | CE2 | TYR- 158 | 4.2 | 0 | Hydrophobic |
| C | CG | MET- 161 | 4.07 | 0 | Hydrophobic |
| F1 | CB | ALA- 198 | 3.41 | 0 | Hydrophobic |
| S1 | CB | ALA- 198 | 3.65 | 0 | Hydrophobic |
| S | CB | ALA- 198 | 4.48 | 0 | Hydrophobic |
| S | CG | MET- 199 | 3.97 | 0 | Hydrophobic |
| C14 | SD | MET- 199 | 3.4 | 0 | Hydrophobic |
| C11 | CB | ILE- 202 | 4.11 | 0 | Hydrophobic |
| C12 | CB | ILE- 202 | 4.03 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 207 | 4.1 | 0 | Hydrophobic |
| F | CD2 | LEU- 207 | 3.4 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 215 | 3.94 | 0 | Hydrophobic |
| O | O3 | NAD- 1270 | 3.45 | 171.41 | H-Bond (Ligand Donor) |
| N | O2D | NAD- 1270 | 2.89 | 154.54 | H-Bond (Protein Donor) |
| C | C4N | NAD- 1270 | 4.06 | 0 | Hydrophobic |
| C5 | C2D | NAD- 1270 | 3.45 | 0 | Hydrophobic |
