sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-11-28
| 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: | 36.174 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.075 | 388.125 |
| % Hydrophobic | % Polar |
|---|---|
| 63.48 | 36.52 |
| According to VolSite | |
| HET Code: | G17 |
|---|---|
| Formula: | C26H21F3N4O |
| Molecular weight: | 462.466 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.91 % |
| Polar Surface area: | 66.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -18.997 | 73.3584 | 135.209 |
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 |
| CAK | CG1 | VAL- 37 | 3.89 | 0 | Hydrophobic |
| CAR | CB | ALA- 50 | 3.77 | 0 | Hydrophobic |
| C5 | CB | ALA- 50 | 3.47 | 0 | Hydrophobic |
| CAO | CD | LYS- 52 | 4.05 | 0 | Hydrophobic |
| CAN | CB | LYS- 52 | 3.61 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 52 | 3.93 | 144.36 | Pi/Cation |
| NAS | OE2 | GLU- 69 | 2.75 | 151 | H-Bond (Ligand Donor) |
| CAZ | CG | GLU- 69 | 3.69 | 0 | Hydrophobic |
| FBH | CG2 | ILE- 72 | 3.9 | 0 | Hydrophobic |
| CAZ | CD1 | LEU- 73 | 4.4 | 0 | Hydrophobic |
| CAO | CD1 | LEU- 73 | 4.06 | 0 | Hydrophobic |
| CAV | CD2 | LEU- 73 | 4.12 | 0 | Hydrophobic |
| FBG | CE2 | PHE- 76 | 4.5 | 0 | Hydrophobic |
| FBH | CD2 | PHE- 76 | 3.88 | 0 | Hydrophobic |
| FBH | CG2 | ILE- 81 | 3.5 | 0 | Hydrophobic |
| CAV | CG2 | ILE- 82 | 4.37 | 0 | Hydrophobic |
| CAQ | CG2 | ILE- 82 | 4.34 | 0 | Hydrophobic |
| CAH | CG1 | ILE- 82 | 3.95 | 0 | Hydrophobic |
| CAN | CG2 | ILE- 101 | 3.91 | 0 | Hydrophobic |
| CAH | CB | ALA- 103 | 4.38 | 0 | Hydrophobic |
| CAR | CB | ALA- 103 | 4.14 | 0 | Hydrophobic |
| N1 | N | MET- 106 | 2.98 | 178.09 | H-Bond (Protein Donor) |
| NAG | O | MET- 106 | 2.92 | 167.81 | H-Bond (Ligand Donor) |
| CBC | CB | ASP- 109 | 4.39 | 0 | Hydrophobic |
| FBF | CD1 | ILE- 138 | 4.37 | 0 | Hydrophobic |
| FBG | CD1 | ILE- 138 | 4.18 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 154 | 4.08 | 0 | Hydrophobic |
| CBC | CD2 | LEU- 154 | 3.62 | 0 | Hydrophobic |
| FBF | CG2 | ILE- 163 | 3.71 | 0 | Hydrophobic |
| CAI | CD1 | LEU- 164 | 3.29 | 0 | Hydrophobic |
| CAJ | CD1 | LEU- 164 | 3.33 | 0 | Hydrophobic |
| FBF | CB | ASP- 165 | 4.32 | 0 | Hydrophobic |
| CAZ | CB | ASP- 165 | 3.6 | 0 | Hydrophobic |
| OBA | N | ASP- 165 | 2.98 | 172.13 | H-Bond (Protein Donor) |
