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
2013-01-25
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_PNECA |
| AC: | P16184 |
| Organism: | Pneumocystis carinii |
| Reign: | Eukaryota |
| TaxID: | 4754 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| X | 100 % |
| B-Factor: | 24.549 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.293 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 68.00 | 32.00 |
| According to VolSite | |
| HET Code: | IXF |
|---|---|
| Formula: | C17H20N6 |
| Molecular weight: | 308.381 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.71 % |
| Polar Surface area: | 93.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| 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 |
|---|---|---|
| -5.22996 | 0.983304 | 11.5148 |
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 |
| NAE | O | ILE- 10 | 2.83 | 165.42 | H-Bond (Ligand Donor) |
| CAI | CD1 | LEU- 25 | 4.38 | 0 | Hydrophobic |
| CAS | CD1 | LEU- 25 | 4.18 | 0 | Hydrophobic |
| NAD | OE2 | GLU- 32 | 2.72 | 172.6 | H-Bond (Ligand Donor) |
| NAD | OE1 | GLU- 32 | 3.44 | 132.78 | H-Bond (Ligand Donor) |
| N3 | OE1 | GLU- 32 | 2.82 | 172.95 | H-Bond (Ligand Donor) |
| CAB | CG2 | ILE- 33 | 4.13 | 0 | Hydrophobic |
| CAH | CD1 | ILE- 33 | 4.12 | 0 | Hydrophobic |
| C5 | CD1 | PHE- 36 | 3.45 | 0 | Hydrophobic |
| CAC | CG2 | THR- 61 | 3.79 | 0 | Hydrophobic |
| CAI | CG1 | ILE- 65 | 4.25 | 0 | Hydrophobic |
| CAA | CB | ASN- 69 | 3.63 | 0 | Hydrophobic |
| CAA | CD2 | LEU- 72 | 3.7 | 0 | Hydrophobic |
| CAF | CD2 | LEU- 72 | 4.06 | 0 | Hydrophobic |
| NAE | O | ILE- 123 | 2.88 | 134.09 | H-Bond (Ligand Donor) |
| CAC | C5N | NDP- 301 | 3.82 | 0 | Hydrophobic |
| NAL | O | HOH- 410 | 3.18 | 151.18 | H-Bond (Protein Donor) |
