sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.830 Å
X-ray
2014-10-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.480 | 7.360 | 7.000 | 0.900 | 8.590 | 3 |
| Name: | Serine/threonine-protein kinase B-raf |
|---|---|
| ID: | BRAF_HUMAN |
| AC: | P15056 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 49.870 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.393 | 779.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.14 | 42.86 |
| According to VolSite | |
| HET Code: | 324 |
|---|---|
| Formula: | C17H14ClF2N3O3S |
| Molecular weight: | 413.826 g/mol |
| DrugBank ID: | DB06999 |
| Buried Surface Area: | 75.15 % |
| Polar Surface area: | 100.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -19.376 | -8.95441 | -13.2162 |
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 |
| CL10 | CG2 | ILE- 463 | 3.75 | 0 | Hydrophobic |
| F19 | CG1 | VAL- 471 | 3.84 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 471 | 4.5 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 471 | 4.2 | 0 | Hydrophobic |
| C14 | CB | ALA- 481 | 4.25 | 0 | Hydrophobic |
| C2 | CB | ALA- 481 | 4.02 | 0 | Hydrophobic |
| C17 | CD | LYS- 483 | 4.44 | 0 | Hydrophobic |
| C15 | CB | LYS- 483 | 3.45 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 505 | 3.71 | 0 | Hydrophobic |
| C25 | CB | LEU- 514 | 4.25 | 0 | Hydrophobic |
| C27 | CB | LEU- 514 | 4.24 | 0 | Hydrophobic |
| F20 | CD2 | LEU- 514 | 3.46 | 0 | Hydrophobic |
| C27 | CB | PHE- 516 | 4.19 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 527 | 3.94 | 0 | Hydrophobic |
| C27 | CG2 | THR- 529 | 3.75 | 0 | Hydrophobic |
| C15 | CG2 | THR- 529 | 3.7 | 0 | Hydrophobic |
| N7 | O | GLN- 530 | 2.73 | 147.55 | H-Bond (Ligand Donor) |
| CL10 | CH2 | TRP- 531 | 3.99 | 0 | Hydrophobic |
| N4 | N | CYS- 532 | 2.99 | 163.49 | H-Bond (Protein Donor) |
| CL10 | CB | SER- 535 | 4.39 | 0 | Hydrophobic |
| F20 | CE1 | PHE- 583 | 3.79 | 0 | Hydrophobic |
| CL10 | CD2 | PHE- 583 | 4.01 | 0 | Hydrophobic |
| C1 | CE2 | PHE- 583 | 3.36 | 0 | Hydrophobic |
| O24 | N | ASP- 594 | 3.2 | 125.81 | H-Bond (Protein Donor) |
| O24 | N | PHE- 595 | 2.84 | 135.92 | H-Bond (Protein Donor) |
| C25 | CZ | PHE- 595 | 4.36 | 0 | Hydrophobic |
| C26 | CE1 | PHE- 595 | 4.02 | 0 | Hydrophobic |
| C27 | CZ | PHE- 595 | 4.24 | 0 | Hydrophobic |
