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
2006-03-09
| 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: | 33.138 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.775 | 297.000 |
| % Hydrophobic | % Polar |
|---|---|
| 63.64 | 36.36 |
| According to VolSite | |
| HET Code: | RAP |
|---|---|
| Formula: | C51H79NO13 |
| Molecular weight: | 914.172 g/mol |
| DrugBank ID: | DB00877 |
| Buried Surface Area: | 36.53 % |
| 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 |
|---|---|---|
| 2.53138 | 11.756 | 11.8121 |
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 | 3.54 | 0 | Hydrophobic |
| C43 | CD1 | PHE- 36 | 3.76 | 0 | Hydrophobic |
| C10 | CB | ASP- 37 | 4.39 | 0 | Hydrophobic |
| O6 | OD1 | ASP- 37 | 2.69 | 167.19 | H-Bond (Ligand Donor) |
| C4 | CE2 | PHE- 46 | 3.78 | 0 | Hydrophobic |
| C5 | CZ | PHE- 46 | 3.96 | 0 | Hydrophobic |
| C44 | CE1 | PHE- 46 | 4.4 | 0 | Hydrophobic |
| C48 | CZ | PHE- 46 | 3.96 | 0 | Hydrophobic |
| O13 | O | GLN- 53 | 2.82 | 165.54 | H-Bond (Ligand Donor) |
| C28 | CG | GLU- 54 | 4.5 | 0 | Hydrophobic |
| C46 | CG | GLU- 54 | 4.13 | 0 | Hydrophobic |
| O10 | O | GLU- 54 | 2.7 | 150.33 | H-Bond (Ligand Donor) |
| C3 | CB | VAL- 55 | 4.16 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 55 | 3.77 | 0 | Hydrophobic |
| O2 | N | ILE- 56 | 2.89 | 149.84 | H-Bond (Protein Donor) |
| C3 | CG1 | ILE- 56 | 4.02 | 0 | Hydrophobic |
| C42 | CG2 | ILE- 56 | 4.01 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 59 | 3.56 | 0 | Hydrophobic |
| O3 | OH | TYR- 82 | 2.67 | 160.96 | H-Bond (Protein Donor) |
| C35 | CE1 | TYR- 82 | 3.79 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 90 | 4.11 | 0 | Hydrophobic |
| C43 | CG2 | ILE- 90 | 3.94 | 0 | Hydrophobic |
| C43 | CG1 | ILE- 91 | 4.19 | 0 | Hydrophobic |
| C3 | CE2 | PHE- 99 | 4.35 | 0 | Hydrophobic |
