sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2007-03-08
| Name: | Trans-aconitate 2-methyltransferase |
|---|---|
| ID: | TAM_AGRFC |
| AC: | Q8UH15 |
| Organism: | Agrobacterium fabrum ) |
| Reign: | Bacteria |
| TaxID: | 176299 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 31.606 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.696 | 1083.375 |
| % Hydrophobic | % Polar |
|---|---|
| 30.84 | 69.16 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 52.97 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -30.68 | 54.2481 | 43.2042 |
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 |
| N | O | GLY- 38 | 2.74 | 161.88 | H-Bond (Ligand Donor) |
| N | OG | SER- 44 | 2.97 | 157.31 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 61 | 2.67 | 165.14 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 61 | 3.4 | 125.35 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 61 | 2.66 | 156.02 | H-Bond (Ligand Donor) |
| N3 | N | SER- 62 | 3.3 | 134.76 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 83 | 3.07 | 157.24 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 84 | 2.96 | 175.16 | H-Bond (Protein Donor) |
| N | O | ASN- 99 | 2.84 | 153.84 | H-Bond (Ligand Donor) |
| O | ND2 | ASN- 99 | 2.83 | 157.43 | H-Bond (Protein Donor) |
| CG | CB | ALA- 100 | 4.2 | 0 | Hydrophobic |
| C5' | CB | VAL- 101 | 4.49 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 101 | 4.15 | 0 | Hydrophobic |
