sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
1995-01-25
| 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: | 28.236 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.437 | 472.500 |
| % Hydrophobic | % Polar |
|---|---|
| 52.86 | 47.14 |
| According to VolSite | |
| HET Code: | MTX |
|---|---|
| Formula: | C20H20N8O5 |
| Molecular weight: | 452.423 g/mol |
| DrugBank ID: | DB00563 |
| Buried Surface Area: | 68.26 % |
| 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 |
|---|---|---|
| 30.6836 | 16.8444 | -1.60939 |
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 | 2.89 | 155.33 | H-Bond (Ligand Donor) |
| CM | CD2 | TYR- 22 | 4.08 | 0 | Hydrophobic |
| N1 | OE1 | GLU- 30 | 2.69 | 173.17 | H-Bond (Ligand Donor) |
| NA2 | OE2 | GLU- 30 | 2.73 | 172.12 | H-Bond (Ligand Donor) |
| NA2 | OE1 | GLU- 30 | 3.39 | 131.11 | H-Bond (Ligand Donor) |
| CB | CD1 | PHE- 31 | 4.28 | 0 | Hydrophobic |
| CB | CB | GLN- 35 | 4.17 | 0 | Hydrophobic |
| CM | CB | SER- 59 | 4.06 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 60 | 4 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 60 | 4.04 | 0 | Hydrophobic |
| O | ND2 | ASN- 64 | 2.64 | 146.03 | H-Bond (Protein Donor) |
| C16 | CD2 | LEU- 67 | 4.27 | 0 | Hydrophobic |
| O1 | CZ | ARG- 70 | 3.67 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 70 | 3.87 | 0 | Ionic (Protein Cationic) |
| O1 | NH2 | ARG- 70 | 2.68 | 166.62 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 70 | 3.12 | 171.61 | H-Bond (Protein Donor) |
| NA4 | O | VAL- 115 | 3.19 | 137.95 | H-Bond (Ligand Donor) |
| C9 | C3N | NDP- 187 | 3.96 | 0 | Hydrophobic |
| N8 | O | HOH- 224 | 3.1 | 140.15 | H-Bond (Protein Donor) |
