sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
1998-07-09
| Name: | Mitogen-activated protein kinase 1 |
|---|---|
| ID: | MK01_RAT |
| AC: | P63086 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 2.7.11.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.032 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.297 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 41.18 | 58.82 |
| According to VolSite | |
| HET Code: | SB4 |
|---|---|
| Formula: | C18H20FN6 |
| Molecular weight: | 339.390 g/mol |
| DrugBank ID: | DB04338 |
| Buried Surface Area: | 56.42 % |
| Polar Surface area: | 86.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -14.2028 | 13.8618 | 40.9622 |
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 |
| CB1 | CG1 | VAL- 37 | 3.8 | 0 | Hydrophobic |
| CB6 | CG2 | VAL- 37 | 4.02 | 0 | Hydrophobic |
| CC1 | CG1 | VAL- 37 | 4.48 | 0 | Hydrophobic |
| CC1 | CB | ALA- 50 | 4.34 | 0 | Hydrophobic |
| CB1 | CB | ALA- 50 | 4.03 | 0 | Hydrophobic |
| CB5 | CD | LYS- 52 | 3.85 | 0 | Hydrophobic |
| CB3 | CB | LYS- 52 | 3.59 | 0 | Hydrophobic |
| CB3 | CG2 | ILE- 101 | 4.25 | 0 | Hydrophobic |
| FB7 | CG1 | ILE- 101 | 4.47 | 0 | Hydrophobic |
| CB2 | CB | GLN- 103 | 4.21 | 0 | Hydrophobic |
| FB7 | CG | GLN- 103 | 3.53 | 0 | Hydrophobic |
| NC7 | OE1 | GLN- 103 | 3.42 | 155.16 | H-Bond (Ligand Donor) |
| NC7 | O | ASP- 104 | 2.79 | 139.3 | H-Bond (Ligand Donor) |
| NC5 | N | MET- 106 | 3.21 | 162.46 | H-Bond (Protein Donor) |
| NA3 | OD2 | ASP- 109 | 2.73 | 149.52 | H-Bond (Ligand Donor) |
| NA3 | OD2 | ASP- 109 | 2.73 | 0 | Ionic (Ligand Cationic) |
| CA1 | CD2 | LEU- 154 | 3.68 | 0 | Hydrophobic |
