sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.950 Å
X-ray
2013-01-22
| Name: | DNA gyrase subunit B |
|---|---|
| ID: | GYRB_MYCTU |
| AC: | P9WG45 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 8 % |
| F | 92 % |
| B-Factor: | 61.648 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.422 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 47.87 | 52.13 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 86.38 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -19.2368 | 16.9228 | 58.5601 |
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 |
| O2' | OH | TYR- 12 | 3.14 | 164.8 | H-Bond (Ligand Donor) |
| N3 | OH | TYR- 12 | 3.03 | 143.56 | H-Bond (Protein Donor) |
| C4' | CD1 | ILE- 17 | 4.45 | 0 | Hydrophobic |
| O2A | ND2 | ASN- 52 | 2.77 | 146.48 | H-Bond (Protein Donor) |
| N6 | OD2 | ASP- 79 | 3.19 | 169.59 | H-Bond (Ligand Donor) |
| C5' | CG1 | VAL- 99 | 3.77 | 0 | Hydrophobic |
| C4' | CG2 | VAL- 99 | 3.87 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 99 | 4.39 | 0 | Hydrophobic |
| O3' | N | GLY- 107 | 2.79 | 168.71 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 108 | 2.82 | 149.49 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 108 | 2.82 | 0 | Ionic (Protein Cationic) |
| C3' | CD | LYS- 108 | 4.26 | 0 | Hydrophobic |
| C2' | CE1 | TYR- 114 | 3.83 | 0 | Hydrophobic |
| O2G | N | LEU- 120 | 2.97 | 161.97 | H-Bond (Protein Donor) |
| O2G | N | HIS- 121 | 3.02 | 167.4 | H-Bond (Protein Donor) |
| O3G | N | VAL- 123 | 2.81 | 157.86 | H-Bond (Protein Donor) |
| O3G | N | GLY- 124 | 2.66 | 168.95 | H-Bond (Protein Donor) |
| O1A | N | VAL- 125 | 3.11 | 137.84 | H-Bond (Protein Donor) |
| O2A | N | VAL- 125 | 3.3 | 150.04 | H-Bond (Protein Donor) |
| C5' | CG1 | VAL- 125 | 4.47 | 0 | Hydrophobic |
| O2G | NE2 | GLN- 370 | 3.33 | 153.01 | H-Bond (Protein Donor) |
| O3G | NE2 | GLN- 370 | 3.06 | 140 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 372 | 3.91 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 372 | 2.8 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 372 | 2.8 | 152.33 | H-Bond (Protein Donor) |
| O1G | MG | MG- 602 | 1.94 | 0 | Metal Acceptor |
