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
2009-04-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.300 | 6.300 | 6.300 | 0.000 | 6.300 | 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: | 17.491 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.014 | 469.125 |
| % Hydrophobic | % Polar |
|---|---|
| 62.59 | 37.41 |
| According to VolSite | |
| HET Code: | 51P |
|---|---|
| Formula: | C16H16N4O2 |
| Molecular weight: | 296.324 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.38 % |
| 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 |
|---|---|---|
| 2.55967 | -3.35381 | 5.88 |
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 | 2.93 | 178.53 | H-Bond (Ligand Donor) |
| N2' | O | VAL- 8 | 3.41 | 127.75 | H-Bond (Ligand Donor) |
| C13 | CG | LEU- 22 | 4.35 | 0 | Hydrophobic |
| N1' | OE1 | GLU- 30 | 3.41 | 133.85 | H-Bond (Ligand Donor) |
| N1' | OE2 | GLU- 30 | 2.74 | 164.36 | H-Bond (Ligand Donor) |
| N2' | OE1 | GLU- 30 | 2.78 | 173.44 | H-Bond (Ligand Donor) |
| C5' | CB | PHE- 34 | 4.4 | 0 | Hydrophobic |
| C5' | CD1 | PHE- 34 | 3.35 | 0 | Hydrophobic |
| C10 | CG2 | THR- 56 | 3.48 | 0 | Hydrophobic |
| C13 | CB | SER- 59 | 4.21 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 60 | 3.69 | 0 | Hydrophobic |
| C'4 | CG2 | ILE- 60 | 4.22 | 0 | Hydrophobic |
| C'1 | CG1 | ILE- 60 | 4.16 | 0 | Hydrophobic |
| C'5 | CD2 | LEU- 67 | 3.84 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 115 | 4.32 | 0 | Hydrophobic |
| N4' | O | VAL- 115 | 3.29 | 135.72 | H-Bond (Ligand Donor) |
| N2' | O | HOH- 194 | 3.45 | 137.32 | H-Bond (Ligand Donor) |
