sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2006-04-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.920 | 6.950 | 6.960 | 0.020 | 6.960 | 4 |
| Name: | Mitogen-activated protein kinase kinase kinase 5 |
|---|---|
| ID: | M3K5_HUMAN |
| AC: | Q99683 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.25 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.177 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.228 | 661.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.90 | 55.10 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 65.21 % |
| Polar Surface area: | 74.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 8 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -2.14497 | 8.10923 | -23.9744 |
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 |
| C19 | CB | LEU- 686 | 4.2 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 686 | 4.06 | 0 | Hydrophobic |
| C20 | CB | LEU- 686 | 3.97 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 686 | 4.1 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 694 | 4.31 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 694 | 3.94 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 694 | 4.05 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 694 | 3.47 | 0 | Hydrophobic |
| C10 | CB | ALA- 707 | 4.26 | 0 | Hydrophobic |
| C14 | CD | LYS- 709 | 4 | 0 | Hydrophobic |
| C13 | SD | MET- 754 | 3.67 | 0 | Hydrophobic |
| N1 | O | GLU- 755 | 2.75 | 160.72 | H-Bond (Ligand Donor) |
| O5 | N | VAL- 757 | 2.78 | 168.41 | H-Bond (Protein Donor) |
| C24 | CB | SER- 761 | 4.49 | 0 | Hydrophobic |
| N4 | O | ASP- 807 | 2.9 | 143.48 | H-Bond (Ligand Donor) |
| C24 | CD2 | LEU- 810 | 4.43 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 810 | 3.93 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 810 | 4.15 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 810 | 3.2 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 810 | 3.84 | 0 | Hydrophobic |
| C27 | CB | SER- 821 | 3.47 | 0 | Hydrophobic |
| C14 | CB | PHE- 823 | 4.07 | 0 | Hydrophobic |
