sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.890 Å
X-ray
2006-01-27
| Name: | Serine/threonine-protein kinase PknB |
|---|---|
| ID: | PKNB_MYCTU |
| AC: | P9WI81 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 79.456 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.419 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.94 | 44.06 |
| According to VolSite | |
| HET Code: | MIX |
|---|---|
| Formula: | C22H28N4O6 |
| Molecular weight: | 444.481 g/mol |
| DrugBank ID: | DB01204 |
| Buried Surface Area: | 50.91 % |
| Polar Surface area: | 177.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 62.2226 | 3.97213 | -24.3372 |
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 |
| CBE | CB | LEU- 17 | 4.12 | 0 | Hydrophobic |
| CAW | CD1 | LEU- 17 | 3.77 | 0 | Hydrophobic |
| CAX | CG1 | VAL- 25 | 3.89 | 0 | Hydrophobic |
| CAG | CB | ALA- 38 | 3.4 | 0 | Hydrophobic |
| CAH | CG1 | VAL- 72 | 4.42 | 0 | Hydrophobic |
| CAH | SD | MET- 92 | 4.27 | 0 | Hydrophobic |
| OAE | N | VAL- 95 | 2.84 | 152.16 | H-Bond (Protein Donor) |
| OAE | O | VAL- 95 | 3.22 | 122.14 | H-Bond (Ligand Donor) |
| CAW | CG2 | VAL- 95 | 4.29 | 0 | Hydrophobic |
| CAI | CG2 | THR- 99 | 4.11 | 0 | Hydrophobic |
| OAD | NZ | LYS- 140 | 3.32 | 144.78 | H-Bond (Protein Donor) |
| NAT | OD1 | ASN- 143 | 2.52 | 131.72 | H-Bond (Ligand Donor) |
| CAQ | CE | MET- 145 | 3.99 | 0 | Hydrophobic |
| CBC | SD | MET- 145 | 4.2 | 0 | Hydrophobic |
| CBE | SD | MET- 145 | 4 | 0 | Hydrophobic |
| CBD | SD | MET- 155 | 4.25 | 0 | Hydrophobic |
| CAR | CE | MET- 155 | 3.72 | 0 | Hydrophobic |
