sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2005-04-20
| Name: | Isoflavone 4'-O-methyltransferase |
|---|---|
| ID: | I4OMT_MEDTR |
| AC: | Q29U70 |
| Organism: | Medicago truncatula |
| Reign: | Eukaryota |
| TaxID: | 3880 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.919 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.604 | 1883.250 |
| % Hydrophobic | % Polar |
|---|---|
| 64.16 | 35.84 |
| According to VolSite | |
| HET Code: | 2HI |
|---|---|
| Formula: | C15H12O5 |
| Molecular weight: | 272.253 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.83 % |
| Polar Surface area: | 86.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 102.401 | 75.811 | 32.6772 |
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 |
| C3 | CB | ALA- 126 | 4.41 | 0 | Hydrophobic |
| C2 | CB | ALA- 178 | 3.68 | 0 | Hydrophobic |
| C13 | SD | MET- 179 | 4.3 | 0 | Hydrophobic |
| C2 | CE | MET- 179 | 3.87 | 0 | Hydrophobic |
| C10 | CE | MET- 179 | 4.34 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 321 | 4.07 | 0 | Hydrophobic |
| C9 | CE | MET- 322 | 4.35 | 0 | Hydrophobic |
| C10 | CE | MET- 322 | 3.88 | 0 | Hydrophobic |
| C9 | SD | MET- 325 | 4.04 | 0 | Hydrophobic |
| C5 | CE | MET- 325 | 4.09 | 0 | Hydrophobic |
| C12 | CE2 | PHE- 326 | 3.49 | 0 | Hydrophobic |
| O5 | O | HOH- 4004 | 2.53 | 164 | H-Bond (Ligand Donor) |
