sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2009-12-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.610 | 7.610 | 7.610 | 0.000 | 7.610 | 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: | 19.179 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.828 | 496.125 |
| % Hydrophobic | % Polar |
|---|---|
| 60.54 | 39.46 |
| According to VolSite | |
| HET Code: | OAG |
|---|---|
| Formula: | C14H12Cl2N6 |
| Molecular weight: | 335.191 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.53 % |
| Polar Surface area: | 102.74 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 14.7792 | 5.52814 | 0.143 |
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 |
| N4' | O | ILE- 7 | 3.13 | 166.54 | H-Bond (Ligand Donor) |
| N2' | O | VAL- 8 | 3.38 | 121.33 | H-Bond (Ligand Donor) |
| N1' | OE2 | GLU- 30 | 2.75 | 168.69 | H-Bond (Ligand Donor) |
| N2' | OE2 | GLU- 30 | 3.48 | 128.98 | H-Bond (Ligand Donor) |
| N2' | OE1 | GLU- 30 | 2.78 | 178.62 | H-Bond (Ligand Donor) |
| C11 | CE1 | PHE- 31 | 3.47 | 0 | Hydrophobic |
| CL5 | CE2 | PHE- 34 | 4.35 | 0 | Hydrophobic |
| C4A | CB | PHE- 34 | 4.41 | 0 | Hydrophobic |
| C6' | CG1 | ILE- 60 | 4.15 | 0 | Hydrophobic |
| C5' | CG2 | ILE- 60 | 4.2 | 0 | Hydrophobic |
| C3' | CG | PRO- 61 | 4.15 | 0 | Hydrophobic |
| C12 | CB | ASN- 64 | 4.12 | 0 | Hydrophobic |
| CL5 | CD2 | LEU- 67 | 3.28 | 0 | Hydrophobic |
| N2' | O | HOH- 205 | 3.36 | 138.86 | H-Bond (Ligand Donor) |
