sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.510 Å
X-ray
2016-01-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.270 | 6.720 | 6.590 | 0.540 | 7.660 | 7 |
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 26.698 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.339 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.65 | 43.35 |
| According to VolSite | |
| HET Code: | BAX |
|---|---|
| Formula: | C21H16ClF3N4O3 |
| Molecular weight: | 464.825 g/mol |
| DrugBank ID: | DB00398 |
| Buried Surface Area: | 65.35 % |
| Polar Surface area: | 92.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 28.5357 | 14.4347 | -13.14 |
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 | CG1 | VAL- 471 | 4.36 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 471 | 4.33 | 0 | Hydrophobic |
| C20 | CB | ALA- 481 | 4.44 | 0 | Hydrophobic |
| C24 | CB | ALA- 481 | 3.35 | 0 | Hydrophobic |
| C20 | CB | LYS- 483 | 4.25 | 0 | Hydrophobic |
| C21 | CD | LYS- 483 | 3.84 | 0 | Hydrophobic |
| C3 | CG | GLU- 501 | 4.06 | 0 | Hydrophobic |
| N12 | OE2 | GLU- 501 | 2.73 | 147.34 | H-Bond (Ligand Donor) |
| N14 | OE2 | GLU- 501 | 2.78 | 145.4 | H-Bond (Ligand Donor) |
| F9 | CG1 | VAL- 504 | 4.15 | 0 | Hydrophobic |
| CL11 | CG1 | VAL- 504 | 3.72 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 504 | 4.02 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 505 | 3.38 | 0 | Hydrophobic |
| F9 | CG2 | THR- 508 | 4.05 | 0 | Hydrophobic |
| F8 | CG2 | ILE- 513 | 3.38 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 514 | 4.33 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 514 | 4.02 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 514 | 3.5 | 0 | Hydrophobic |
| C21 | CG2 | THR- 529 | 3.85 | 0 | Hydrophobic |
| N30 | O | CYS- 532 | 2.8 | 148.64 | H-Bond (Ligand Donor) |
| N26 | N | CYS- 532 | 3.19 | 161.62 | H-Bond (Protein Donor) |
| F9 | CD2 | LEU- 567 | 3.72 | 0 | Hydrophobic |
| F10 | CD1 | LEU- 567 | 3.63 | 0 | Hydrophobic |
| CL11 | CG2 | ILE- 572 | 3.89 | 0 | Hydrophobic |
| F10 | CG2 | ILE- 592 | 4 | 0 | Hydrophobic |
| C1 | CB | ASP- 594 | 4.3 | 0 | Hydrophobic |
| C3 | CB | ASP- 594 | 3.75 | 0 | Hydrophobic |
| O15 | N | ASP- 594 | 2.69 | 169.04 | H-Bond (Protein Donor) |
