sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2010-07-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.960 | 5.960 | 5.960 | 0.000 | 5.960 | 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: | 22.496 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.013 | 516.375 |
| % Hydrophobic | % Polar |
|---|---|
| 62.75 | 37.25 |
| According to VolSite | |
| HET Code: | D2H |
|---|---|
| Formula: | C19H22N4O2 |
| Molecular weight: | 338.404 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.63 % |
| 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: | 5 |
| X | Y | Z |
|---|---|---|
| -3.5874 | 16.3314 | 25.9258 |
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 |
| CAB | CD1 | LEU- 22 | 3.48 | 0 | Hydrophobic |
| CAI | CG | LEU- 22 | 3.5 | 0 | Hydrophobic |
| CAV | CD2 | LEU- 22 | 4.03 | 0 | Hydrophobic |
| N1 | OE1 | GLU- 30 | 3.47 | 129.02 | H-Bond (Ligand Donor) |
| N1 | OE2 | GLU- 30 | 2.77 | 172.62 | H-Bond (Ligand Donor) |
| NAD | OE1 | GLU- 30 | 2.71 | 169.02 | H-Bond (Ligand Donor) |
| NAE | OE2 | GLU- 30 | 3.45 | 131.73 | H-Bond (Ligand Donor) |
| CAB | CD1 | PHE- 31 | 3.86 | 0 | Hydrophobic |
| CAC | CE1 | PHE- 31 | 3.45 | 0 | Hydrophobic |
| CAA | CZ | PHE- 34 | 3.74 | 0 | Hydrophobic |
| CAC | CE2 | PHE- 34 | 4.03 | 0 | Hydrophobic |
| CAY | CZ | PHE- 34 | 4.12 | 0 | Hydrophobic |
| CAA | CG2 | THR- 56 | 3.85 | 0 | Hydrophobic |
| CAH | CB | SER- 59 | 3.83 | 0 | Hydrophobic |
| CAA | CD1 | ILE- 60 | 4.48 | 0 | Hydrophobic |
| CAC | CG1 | ILE- 60 | 4.47 | 0 | Hydrophobic |
| CAL | CG1 | ILE- 60 | 4.01 | 0 | Hydrophobic |
| CAA | CD1 | LEU- 67 | 4.46 | 0 | Hydrophobic |
| CAC | CD2 | LEU- 67 | 4.46 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 115 | 3.54 | 0 | Hydrophobic |
| CAH | C2D | NDP- 187 | 3.84 | 0 | Hydrophobic |
| NAE | O | HOH- 213 | 2.97 | 137.98 | H-Bond (Ligand Donor) |
