sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.790 Å
X-ray
2015-07-06
| Name: | Stress-activated protein kinase JNK |
|---|---|
| ID: | JNK_DROME |
| AC: | P92208 |
| Organism: | Drosophila melanogaster |
| Reign: | Eukaryota |
| TaxID: | 7227 |
| EC Number: | 2.7.11.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 23.771 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.730 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.58 | 42.42 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.69 % |
| 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 |
|---|---|---|
| -11.6636 | -0.473226 | 17.1484 |
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 |
| C1' | CD1 | ILE- 30 | 4.06 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 38 | 3.83 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 38 | 4.49 | 0 | Hydrophobic |
| O3G | NZ | LYS- 53 | 3.04 | 159.39 | H-Bond (Protein Donor) |
| O2A | NZ | LYS- 53 | 2.99 | 161.11 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 53 | 3.04 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 53 | 2.99 | 0 | Ionic (Protein Cationic) |
| N6 | O | GLU- 107 | 3.05 | 149.03 | H-Bond (Ligand Donor) |
| N1 | N | MET- 109 | 3.03 | 163.28 | H-Bond (Protein Donor) |
| O3' | ND2 | ASN- 112 | 3.49 | 140.4 | H-Bond (Protein Donor) |
| O2' | ND2 | ASN- 112 | 2.98 | 147.5 | H-Bond (Protein Donor) |
| C2' | CB | ASN- 112 | 4.02 | 0 | Hydrophobic |
| O3' | O | SER- 153 | 2.62 | 144.55 | H-Bond (Ligand Donor) |
| O2G | ND2 | ASN- 154 | 3.38 | 120.97 | H-Bond (Protein Donor) |
| C2' | CG1 | VAL- 156 | 4.15 | 0 | Hydrophobic |
| C3' | CD1 | LEU- 166 | 4.26 | 0 | Hydrophobic |
| O2G | MG | MG- 402 | 1.9 | 0 | Metal Acceptor |
| O1B | MG | MG- 402 | 2.04 | 0 | Metal Acceptor |
| O1A | MG | MG- 402 | 2.07 | 0 | Metal Acceptor |
| O3G | MG | MG- 403 | 2.16 | 0 | Metal Acceptor |
