sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2006-03-08
| 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 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: | 26.533 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.527 | 246.375 |
| % Hydrophobic | % Polar |
|---|---|
| 50.68 | 49.32 |
| According to VolSite | |
| HET Code: | RAP |
|---|---|
| Formula: | C51H79NO13 |
| Molecular weight: | 914.172 g/mol |
| DrugBank ID: | DB00877 |
| Buried Surface Area: | 37.16 % |
| 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 |
|---|---|---|
| 2.7352 | 11.7524 | 12.3956 |
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 | 3.55 | 0 | Hydrophobic |
| C43 | CD1 | PHE- 36 | 3.95 | 0 | Hydrophobic |
| C10 | CB | ASP- 37 | 4.33 | 0 | Hydrophobic |
| O6 | OD2 | ASP- 37 | 2.62 | 164.11 | H-Bond (Ligand Donor) |
| C4 | CE2 | PHE- 46 | 3.81 | 0 | Hydrophobic |
| C5 | CZ | PHE- 46 | 3.95 | 0 | Hydrophobic |
| C44 | CE1 | PHE- 46 | 4.1 | 0 | Hydrophobic |
| C48 | CE1 | PHE- 46 | 3.76 | 0 | Hydrophobic |
| O13 | O | GLN- 53 | 2.68 | 158.21 | H-Bond (Ligand Donor) |
| O10 | O | GLU- 54 | 2.77 | 142.14 | H-Bond (Ligand Donor) |
| C46 | CG | GLU- 54 | 4.08 | 0 | Hydrophobic |
| C3 | CB | VAL- 55 | 4.1 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 55 | 3.78 | 0 | Hydrophobic |
| O2 | N | ILE- 56 | 2.9 | 152.91 | H-Bond (Protein Donor) |
| C3 | CG1 | ILE- 56 | 3.98 | 0 | Hydrophobic |
| C42 | CG2 | ILE- 56 | 4.14 | 0 | Hydrophobic |
| C3 | CD1 | PHE- 59 | 3.56 | 0 | Hydrophobic |
| C4 | CG | PHE- 59 | 3.76 | 0 | Hydrophobic |
| C5 | CE1 | PHE- 59 | 4.17 | 0 | Hydrophobic |
| O3 | OH | TYR- 82 | 2.63 | 169.45 | H-Bond (Protein Donor) |
| C49 | CE1 | TYR- 82 | 4.04 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 90 | 4.05 | 0 | Hydrophobic |
| C43 | CG2 | ILE- 90 | 3.94 | 0 | Hydrophobic |
| C43 | CG1 | ILE- 91 | 4.31 | 0 | Hydrophobic |
| C3 | CZ | PHE- 99 | 4.37 | 0 | Hydrophobic |
