sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.530 Å
X-ray
2011-05-18
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.340 | 5.840 | 5.860 | 1.140 | 8.000 | 9 |
| 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: | 11.673 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.391 | 931.500 |
| % Hydrophobic | % Polar |
|---|---|
| 59.42 | 40.58 |
| According to VolSite | |
| HET Code: | TOP |
|---|---|
| Formula: | C14H18N4O3 |
| Molecular weight: | 290.318 g/mol |
| DrugBank ID: | DB00440 |
| Buried Surface Area: | 66.48 % |
| Polar Surface area: | 105.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 15.0739 | 6.98329 | 0.431333 |
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 |
| N7 | O | ILE- 7 | 3.21 | 166 | H-Bond (Ligand Donor) |
| N2 | OE2 | GLU- 30 | 2.72 | 164.34 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 30 | 3.42 | 134.39 | H-Bond (Ligand Donor) |
| N4 | OE1 | GLU- 30 | 2.86 | 162.29 | H-Bond (Ligand Donor) |
| C14 | CG | PHE- 31 | 3.5 | 0 | Hydrophobic |
| C11 | CB | PHE- 34 | 4.5 | 0 | Hydrophobic |
| C14 | CD2 | PHE- 34 | 3.64 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 34 | 3.67 | 0 | Aromatic Face/Face |
| DuAr | DuAr | PHE- 34 | 3.67 | 0 | Aromatic Face/Face |
| O13 | NZ | LYS- 35 | 3.35 | 155.4 | H-Bond (Protein Donor) |
| C14 | CD | LYS- 35 | 3.57 | 0 | Hydrophobic |
| C20 | SD | MET- 52 | 4.4 | 0 | Hydrophobic |
| C20 | CG2 | THR- 56 | 3.7 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 60 | 3.5 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 60 | 3.82 | 0 | Hydrophobic |
| C17 | CB | PHE- 64 | 4.1 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 67 | 4.38 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 67 | 3.61 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 115 | 3.62 | 0 | Hydrophobic |
| N4 | O | HOH- 196 | 3.23 | 132.94 | H-Bond (Ligand Donor) |
