sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2014-11-26
| Name: | D-mycarose 3-C-methyltransferase |
|---|---|
| ID: | Q194Q4_STRAA |
| AC: | Q194Q4 |
| Organism: | Streptomyces argillaceus |
| Reign: | Bacteria |
| TaxID: | 41951 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 62.141 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.487 | 1893.375 |
| % Hydrophobic | % Polar |
|---|---|
| 47.59 | 52.41 |
| According to VolSite | |
| HET Code: | TYD |
|---|---|
| Formula: | C10H13N2O11P2 |
| Molecular weight: | 399.165 g/mol |
| DrugBank ID: | DB03103 |
| Buried Surface Area: | 56.62 % |
| Polar Surface area: | 220.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -17.0791 | 5.40616 | 12.0534 |
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 |
| O3B | ND1 | HIS- 255 | 3.23 | 122.19 | H-Bond (Protein Donor) |
| C4' | CB | PRO- 328 | 4.02 | 0 | Hydrophobic |
| O2A | N | ALA- 329 | 3.45 | 156.27 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 330 | 3.25 | 168.62 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 330 | 3.25 | 0 | Ionic (Protein Cationic) |
| O3' | OD2 | ASP- 350 | 2.67 | 141.66 | H-Bond (Ligand Donor) |
| O2 | N | THR- 351 | 3.03 | 152.5 | H-Bond (Protein Donor) |
| O3' | OG1 | THR- 352 | 3.39 | 164.7 | H-Bond (Protein Donor) |
| O3' | NZ | LYS- 355 | 2.73 | 173.28 | H-Bond (Protein Donor) |
| O2B | ND2 | ASN- 387 | 3.4 | 142.29 | H-Bond (Protein Donor) |
| O1B | OH | TYR- 388 | 2.7 | 171.95 | H-Bond (Protein Donor) |
| C5' | CE2 | TYR- 388 | 4.01 | 0 | Hydrophobic |
| C5M | CB | TYR- 388 | 3.68 | 0 | Hydrophobic |
| C5M | CG1 | ILE- 392 | 4.26 | 0 | Hydrophobic |
| O4 | NZ | LYS- 395 | 2.65 | 168.35 | H-Bond (Protein Donor) |
| O3A | O | HOH- 601 | 3.45 | 179.96 | H-Bond (Protein Donor) |
