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
2002-05-22
| 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: | 0.000 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.115 | 401.625 |
| % Hydrophobic | % Polar |
|---|---|
| 63.87 | 36.13 |
| According to VolSite | |
| HET Code: | TRR |
|---|---|
| Formula: | C14H18N4O3 |
| Molecular weight: | 290.318 g/mol |
| DrugBank ID: | DB03125 |
| Buried Surface Area: | 59 % |
| 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 |
|---|---|---|
| 1.75067 | -6.84824 | 0.434667 |
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 | 3.02 | 148.47 | H-Bond (Ligand Donor) |
| C17 | CD1 | LEU- 19 | 3.35 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 19 | 3.6 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 26 | 2.92 | 164.54 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 26 | 2.98 | 170.16 | H-Bond (Ligand Donor) |
| C18 | CD2 | LEU- 27 | 3.29 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 27 | 3.56 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 27 | 3.5 | 0 | Hydrophobic |
| C7 | CZ | PHE- 30 | 4.31 | 0 | Hydrophobic |
| C19 | CD2 | PHE- 30 | 3.34 | 0 | Hydrophobic |
| C7 | CZ | PHE- 49 | 4.18 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 49 | 3.57 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 49 | 3.43 | 0 | Hydrophobic |
| C14 | CG | PRO- 50 | 4.04 | 0 | Hydrophobic |
| C18 | CG | PRO- 50 | 3.51 | 0 | Hydrophobic |
| C7 | C4N | NDP- 168 | 3.4 | 0 | Hydrophobic |
