sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
2006-07-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.880 | 6.880 | 6.880 | 0.000 | 6.880 | 1 |
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_LACCA |
| AC: | P00381 |
| Organism: | Lactobacillus casei |
| Reign: | Bacteria |
| TaxID: | 1582 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 1.000 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.545 | 907.875 |
| % Hydrophobic | % Polar |
|---|---|
| 62.83 | 37.17 |
| According to VolSite | |
| HET Code: | TRR |
|---|---|
| Formula: | C14H18N4O3 |
| Molecular weight: | 290.318 g/mol |
| DrugBank ID: | DB03125 |
| Buried Surface Area: | 63.37 % |
| 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 |
|---|---|---|
| 4.95157 | 2.14705 | -4.3911 |
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 | LEU- 4 | 2.76 | 150.92 | H-Bond (Ligand Donor) |
| O15 | N | LEU- 19 | 3.38 | 156.58 | H-Bond (Protein Donor) |
| C18 | CB | LEU- 19 | 3.72 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 19 | 3.53 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 19 | 3.51 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 19 | 3.92 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 26 | 3.18 | 163.62 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 26 | 2.9 | 172.74 | H-Bond (Ligand Donor) |
| C17 | CD2 | LEU- 27 | 3.91 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 27 | 3.72 | 0 | Hydrophobic |
| C7 | CD1 | PHE- 30 | 3.24 | 0 | Hydrophobic |
| C17 | CD2 | PHE- 30 | 4.14 | 0 | Hydrophobic |
| C12 | CD2 | PHE- 30 | 3.48 | 0 | Hydrophobic |
| C5 | CG | PHE- 30 | 3.13 | 0 | Hydrophobic |
| C19 | CB | SER- 48 | 3.66 | 0 | Hydrophobic |
| C17 | CG | PRO- 50 | 3.89 | 0 | Hydrophobic |
