sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1999-08-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.700 | 9.700 | 9.700 | 0.000 | 9.700 | 1 |
| Name: | Peptidyl-prolyl cis-trans isomerase FKBP1B |
|---|---|
| ID: | FKB1B_HUMAN |
| AC: | P68106 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 5.2.1.8 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.316 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.503 | 249.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | RAP |
|---|---|
| Formula: | C51H79NO13 |
| Molecular weight: | 914.172 g/mol |
| DrugBank ID: | DB00877 |
| Buried Surface Area: | 36.15 % |
| Polar Surface area: | 195.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 13 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -20.1616 | -11.7947 | -11.6817 |
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 |
| C5 | CZ | TYR- 26 | 3.64 | 0 | Hydrophobic |
| C10 | CE1 | PHE- 36 | 4.42 | 0 | Hydrophobic |
| C43 | CE1 | PHE- 36 | 3.98 | 0 | Hydrophobic |
| C10 | CB | ASP- 37 | 4.25 | 0 | Hydrophobic |
| O6 | OD2 | ASP- 37 | 2.7 | 162.12 | H-Bond (Ligand Donor) |
| C44 | CE1 | PHE- 46 | 4.48 | 0 | Hydrophobic |
| C48 | CE1 | PHE- 46 | 3.84 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 46 | 3.63 | 0 | Hydrophobic |
| O13 | O | GLN- 53 | 2.61 | 154.85 | H-Bond (Ligand Donor) |
| O10 | O | GLU- 54 | 2.78 | 163.04 | H-Bond (Ligand Donor) |
| C3 | CB | VAL- 55 | 3.99 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 55 | 3.77 | 0 | Hydrophobic |
| O2 | N | ILE- 56 | 2.78 | 155.44 | H-Bond (Protein Donor) |
| C3 | CG1 | ILE- 56 | 4 | 0 | Hydrophobic |
| C42 | CG2 | ILE- 56 | 4.03 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 59 | 4.11 | 0 | Hydrophobic |
| C3 | CD2 | PHE- 59 | 3.49 | 0 | Hydrophobic |
| O3 | OH | TYR- 82 | 2.69 | 169.49 | H-Bond (Protein Donor) |
| C49 | CE1 | TYR- 82 | 3.87 | 0 | Hydrophobic |
| C43 | CG1 | VAL- 90 | 3.91 | 0 | Hydrophobic |
| C43 | CG1 | ILE- 91 | 3.93 | 0 | Hydrophobic |
| C3 | CZ | PHE- 99 | 4.38 | 0 | Hydrophobic |
