sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.950 Å
X-ray
2004-02-05
| 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: | 52.751 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.287 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 59.21 | 40.79 |
| According to VolSite | |
| HET Code: | BAX |
|---|---|
| Formula: | C21H16ClF3N4O3 |
| Molecular weight: | 464.825 g/mol |
| DrugBank ID: | DB00398 |
| Buried Surface Area: | 66.07 % |
| 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 |
|---|---|---|
| 75.1533 | 44.8326 | 65.0258 |
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- 470 | 4.26 | 0 | Hydrophobic |
| C18 | CB | ALA- 480 | 4.14 | 0 | Hydrophobic |
| C24 | CB | ALA- 480 | 3.5 | 0 | Hydrophobic |
| C17 | CD | LYS- 482 | 4.14 | 0 | Hydrophobic |
| C18 | CB | LYS- 482 | 4.42 | 0 | Hydrophobic |
| C3 | CG | GLU- 500 | 3.85 | 0 | Hydrophobic |
| N12 | OE2 | GLU- 500 | 3.18 | 131.87 | H-Bond (Ligand Donor) |
| N14 | OE2 | GLU- 500 | 3 | 136.32 | H-Bond (Ligand Donor) |
| F8 | CG1 | VAL- 503 | 4.2 | 0 | Hydrophobic |
| CL11 | CG1 | VAL- 503 | 3.72 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 503 | 4.11 | 0 | Hydrophobic |
| F10 | CD2 | LEU- 504 | 4.14 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 504 | 3.45 | 0 | Hydrophobic |
| F8 | CG2 | THR- 507 | 4.06 | 0 | Hydrophobic |
| F8 | CG2 | ILE- 512 | 4.43 | 0 | Hydrophobic |
| F10 | CG2 | ILE- 512 | 3.77 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 513 | 4.08 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 513 | 3.58 | 0 | Hydrophobic |
| C17 | CG2 | THR- 528 | 3.59 | 0 | Hydrophobic |
| N26 | N | CYS- 531 | 2.91 | 152.87 | H-Bond (Protein Donor) |
| F8 | CD2 | LEU- 566 | 3.51 | 0 | Hydrophobic |
| F9 | CD1 | LEU- 566 | 3.5 | 0 | Hydrophobic |
| CL11 | CG2 | ILE- 571 | 3.8 | 0 | Hydrophobic |
| F9 | CG2 | ILE- 591 | 4.38 | 0 | Hydrophobic |
| C1 | CB | ASP- 593 | 4.33 | 0 | Hydrophobic |
| C3 | CB | ASP- 593 | 3.72 | 0 | Hydrophobic |
| O15 | N | ASP- 593 | 3.14 | 170.23 | H-Bond (Protein Donor) |
| C20 | CB | PHE- 594 | 4.34 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 594 | 3.43 | 0 | Hydrophobic |
