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
2010-07-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.890 | 5.890 | 5.890 | 0.000 | 5.890 | 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: | 11.943 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.899 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 59.12 | 40.88 |
| According to VolSite | |
| HET Code: | D2E |
|---|---|
| Formula: | C18H18N4O2 |
| Molecular weight: | 322.361 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.17 % |
| Polar Surface area: | 100.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 15.2734 | 5.91571 | -0.328 |
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 |
| NAB | O | VAL- 8 | 3.18 | 125.8 | H-Bond (Ligand Donor) |
| CAA | CD2 | LEU- 22 | 3.6 | 0 | Hydrophobic |
| N1 | OE2 | GLU- 30 | 2.64 | 171.88 | H-Bond (Ligand Donor) |
| NAB | OE1 | GLU- 30 | 2.8 | 168.36 | H-Bond (Ligand Donor) |
| NAC | OE2 | GLU- 30 | 3.36 | 128.76 | H-Bond (Ligand Donor) |
| CAH | CE1 | PHE- 31 | 3.45 | 0 | Hydrophobic |
| C5 | CB | PHE- 34 | 4.08 | 0 | Hydrophobic |
| CAJ | CZ | PHE- 34 | 4.44 | 0 | Hydrophobic |
| C5 | CD1 | PHE- 34 | 3.44 | 0 | Hydrophobic |
| CAK | CG2 | THR- 56 | 3.45 | 0 | Hydrophobic |
| CAE | CG2 | ILE- 60 | 3.91 | 0 | Hydrophobic |
| CAK | CG1 | ILE- 60 | 3.55 | 0 | Hydrophobic |
| CAU | CG1 | ILE- 60 | 4.02 | 0 | Hydrophobic |
| CAF | CD2 | LEU- 67 | 3.6 | 0 | Hydrophobic |
| CAJ | CG2 | VAL- 115 | 4.05 | 0 | Hydrophobic |
| NAB | OG1 | THR- 136 | 3.44 | 121.26 | H-Bond (Ligand Donor) |
| CAX | C5N | NDP- 187 | 4.21 | 0 | Hydrophobic |
| NAB | O | HOH- 193 | 3.36 | 133.68 | H-Bond (Ligand Donor) |
