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
2010-08-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.610 | 7.610 | 7.610 | 0.000 | 7.610 | 1 |
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_HUMAN |
| AC: | P00374 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 14.847 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.401 | 813.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.92 | 41.08 |
| According to VolSite | |
| HET Code: | OAG |
|---|---|
| Formula: | C14H12Cl2N6 |
| Molecular weight: | 335.191 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.02 % |
| Polar Surface area: | 102.74 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -3.55145 | -15.3912 | 0.0959545 |
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 |
| N4' | O | ILE- 7 | 3.07 | 167.63 | H-Bond (Ligand Donor) |
| N2' | O | VAL- 8 | 3.36 | 122.72 | H-Bond (Ligand Donor) |
| C12 | CG | LEU- 22 | 4.21 | 0 | Hydrophobic |
| CL5 | CG | LEU- 22 | 3.85 | 0 | Hydrophobic |
| N1' | OE2 | GLU- 30 | 2.67 | 170.17 | H-Bond (Ligand Donor) |
| N2' | OE1 | GLU- 30 | 2.72 | 172.33 | H-Bond (Ligand Donor) |
| N2' | OE2 | GLU- 30 | 3.48 | 125.15 | H-Bond (Ligand Donor) |
| CL2 | CE2 | PHE- 31 | 3.55 | 0 | Hydrophobic |
| C4A | CB | PHE- 34 | 4.3 | 0 | Hydrophobic |
| C4A | CD1 | PHE- 34 | 3.46 | 0 | Hydrophobic |
| CL5 | CB | SER- 59 | 3.93 | 0 | Hydrophobic |
| C3' | CG | PRO- 61 | 3.96 | 0 | Hydrophobic |
| CL2 | CD1 | PHE- 64 | 4.17 | 0 | Hydrophobic |
