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
2004-08-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.360 | 9.120 | 9.960 | 1.890 | 10.420 | 5 |
| 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: | 21.814 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.881 | 637.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.14 | 42.86 |
| According to VolSite | |
| HET Code: | MTX |
|---|---|
| Formula: | C20H20N8O5 |
| Molecular weight: | 452.423 g/mol |
| DrugBank ID: | DB00563 |
| Buried Surface Area: | 67.46 % |
| Polar Surface area: | 216.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 30.6207 | 16.8765 | -1.62355 |
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 |
| NA4 | O | ILE- 7 | 2.72 | 147.04 | H-Bond (Ligand Donor) |
| CM | CD1 | LEU- 22 | 4.32 | 0 | Hydrophobic |
| N1 | OE2 | GLU- 30 | 2.94 | 174.89 | H-Bond (Ligand Donor) |
| NA2 | OE1 | GLU- 30 | 3.31 | 167.65 | H-Bond (Ligand Donor) |
| CB | CB | PHE- 31 | 4.48 | 0 | Hydrophobic |
| CB | CB | GLN- 35 | 3.84 | 0 | Hydrophobic |
| C9 | CG2 | THR- 56 | 4.26 | 0 | Hydrophobic |
| CM | CB | SER- 59 | 4.06 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 60 | 3.96 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 60 | 4.21 | 0 | Hydrophobic |
| C16 | CG | PRO- 61 | 4.41 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 67 | 4.03 | 0 | Hydrophobic |
| O1 | CZ | ARG- 70 | 3.62 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 70 | 3.15 | 0 | Ionic (Protein Cationic) |
| O1 | NH2 | ARG- 70 | 2.66 | 166.64 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 70 | 3.1 | 124.41 | H-Bond (Protein Donor) |
| NA4 | O | VAL- 115 | 3.21 | 140.56 | H-Bond (Ligand Donor) |
| NA2 | OG1 | THR- 136 | 3.48 | 123.69 | H-Bond (Ligand Donor) |
| C9 | C5N | NDP- 187 | 4.12 | 0 | Hydrophobic |
