sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2009-10-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.800 | 6.800 | 6.800 | 0.000 | 6.800 | 1 |
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_MOUSE |
| AC: | P00375 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.152 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.222 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 60.54 | 39.46 |
| According to VolSite | |
| HET Code: | D09 |
|---|---|
| Formula: | C16H16N4O2 |
| Molecular weight: | 296.324 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.75 % |
| Polar Surface area: | 100.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -4.13086 | 2.06573 | 13.8 |
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 |
| N2' | O | VAL- 8 | 3 | 134.43 | H-Bond (Ligand Donor) |
| N2' | OE2 | GLU- 30 | 3.5 | 129.83 | H-Bond (Ligand Donor) |
| N2' | OE1 | GLU- 30 | 2.72 | 167.43 | H-Bond (Ligand Donor) |
| N3' | OE2 | GLU- 30 | 2.75 | 167.61 | H-Bond (Ligand Donor) |
| N3' | OE1 | GLU- 30 | 3.47 | 128.38 | H-Bond (Ligand Donor) |
| C'6 | CE1 | PHE- 31 | 3.43 | 0 | Hydrophobic |
| C5' | CB | PHE- 34 | 4.29 | 0 | Hydrophobic |
| C5' | CD1 | PHE- 34 | 3.45 | 0 | Hydrophobic |
| C10 | CG2 | THR- 56 | 3.76 | 0 | Hydrophobic |
| C13 | CB | SER- 59 | 3.77 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 60 | 4.39 | 0 | Hydrophobic |
| C'4 | CG2 | ILE- 60 | 3.88 | 0 | Hydrophobic |
| C'6 | CG1 | ILE- 60 | 4.08 | 0 | Hydrophobic |
| C'6 | CD2 | LEU- 67 | 3.93 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 115 | 4.5 | 0 | Hydrophobic |
| N2' | OG1 | THR- 136 | 3.45 | 121.27 | H-Bond (Ligand Donor) |
| C10 | C5N | NDP- 187 | 4.18 | 0 | Hydrophobic |
