sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.670 Å
X-ray
2011-09-20
| Name: | Multifunctional cyclase-dehydratase-3-O-methyl transferase TcmN |
|---|---|
| ID: | TCMN_STRGA |
| AC: | P16559 |
| Organism: | Streptomyces glaucescens |
| Reign: | Bacteria |
| TaxID: | 1907 |
| EC Number: | 2.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.492 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.044 | 816.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.20 | 43.80 |
| According to VolSite | |
| HET Code: | DQH |
|---|---|
| Formula: | C15H11O7 |
| Molecular weight: | 303.244 g/mol |
| DrugBank ID: | DB02224 |
| Buried Surface Area: | 62.63 % |
| Polar Surface area: | 130.28 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 62.0688 | 6.60336 | 25.6035 |
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 |
| C10 | CB | ASP- 57 | 4.31 | 0 | Hydrophobic |
| O27 | OD2 | ASP- 57 | 2.72 | 155.03 | H-Bond (Ligand Donor) |
| C16 | CB | TRP- 63 | 4.39 | 0 | Hydrophobic |
| C16 | CD2 | TRP- 63 | 3.43 | 0 | Hydrophobic |
| O23 | NH2 | ARG- 82 | 2.57 | 146.27 | H-Bond (Protein Donor) |
| O24 | NH1 | ARG- 82 | 2.53 | 169.36 | H-Bond (Protein Donor) |
| O24 | NH2 | ARG- 82 | 3.23 | 126.66 | H-Bond (Protein Donor) |
| C16 | CG | PRO- 87 | 3.88 | 0 | Hydrophobic |
| C10 | CZ | PHE- 120 | 4.18 | 0 | Hydrophobic |
| C11 | CE1 | PHE- 120 | 4.47 | 0 | Hydrophobic |
| C5 | CB | PHE- 120 | 3.89 | 0 | Hydrophobic |
| C4 | CE | MET- 125 | 4.15 | 0 | Hydrophobic |
| C5 | SD | MET- 125 | 3.83 | 0 | Hydrophobic |
| C19 | CE | MET- 125 | 4.34 | 0 | Hydrophobic |
| C14 | CE | MET- 125 | 4.09 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 128 | 3.71 | 0 | Aromatic Face/Face |
| C6 | CB | HIS- 128 | 3.57 | 0 | Hydrophobic |
| C5 | CB | HIS- 128 | 3.77 | 0 | Hydrophobic |
