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
1993-08-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.770 | 7.920 | 8.000 | 0.110 | 8.000 | 3 |
| Name: | Peptidyl-prolyl cis-trans isomerase FKBP1A |
|---|---|
| ID: | FKB1A_HUMAN |
| AC: | P62942 |
| 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: | 4.577 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.743 | 246.375 |
| % Hydrophobic | % Polar |
|---|---|
| 56.16 | 43.84 |
| According to VolSite | |
| HET Code: | SB3 |
|---|---|
| Formula: | C28H35NO4 |
| Molecular weight: | 449.582 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.87 % |
| Polar Surface area: | 63.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -26.2451 | 28.5399 | 5.24915 |
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 | 3.59 | 0 | Hydrophobic |
| C13 | CE1 | PHE- 36 | 4.46 | 0 | Hydrophobic |
| C14 | CD1 | PHE- 36 | 4.41 | 0 | Hydrophobic |
| C14 | CB | ASP- 37 | 3.67 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 46 | 3.55 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 55 | 3.93 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 56 | 4.34 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 56 | 4.35 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 56 | 3.76 | 0 | Hydrophobic |
| O1 | N | ILE- 56 | 2.89 | 137.17 | H-Bond (Protein Donor) |
| C3 | CE2 | TRP- 59 | 3.39 | 0 | Hydrophobic |
| C4 | CZ3 | TRP- 59 | 3.71 | 0 | Hydrophobic |
| C5 | CH2 | TRP- 59 | 4.14 | 0 | Hydrophobic |
| O3 | OH | TYR- 82 | 2.63 | 171.85 | H-Bond (Protein Donor) |
| C13 | CZ | TYR- 82 | 4.44 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 82 | 3.76 | 0 | Hydrophobic |
| C3 | CZ | PHE- 99 | 4.33 | 0 | Hydrophobic |
