sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2003-09-29
| Name: | 6-phospho-beta-glucosidase BglT |
|---|---|
| ID: | BGLT_THEMA |
| AC: | Q9X108 |
| Organism: | Thermotoga maritima |
| Reign: | Bacteria |
| TaxID: | 243274 |
| EC Number: | 3.2.1.86 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.528 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.996 | 1198.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.92 | 54.08 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.43 % |
| Polar Surface area: | 343.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 99.5496 | 60.3287 | 121.941 |
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 |
| C5B | CB | SER- 10 | 3.88 | 0 | Hydrophobic |
| O2N | OG | SER- 10 | 2.55 | 155.49 | H-Bond (Protein Donor) |
| C4N | CE2 | TYR- 12 | 3.24 | 0 | Hydrophobic |
| O3B | OD2 | ASP- 36 | 2.68 | 164.98 | H-Bond (Ligand Donor) |
| O3B | OD1 | ASP- 36 | 3.37 | 137.77 | H-Bond (Ligand Donor) |
| O2B | OD1 | ASP- 36 | 2.66 | 168.39 | H-Bond (Ligand Donor) |
| O2A | NZ | LYS- 41 | 3.53 | 0 | Ionic (Protein Cationic) |
| C1B | CB | PHE- 79 | 4.06 | 0 | Hydrophobic |
| O4B | N | ARG- 80 | 3.46 | 151.3 | H-Bond (Protein Donor) |
| O3 | NH2 | ARG- 80 | 3.24 | 127.23 | H-Bond (Protein Donor) |
| O3 | NE | ARG- 80 | 2.99 | 134.38 | H-Bond (Protein Donor) |
| O1N | NH2 | ARG- 80 | 2.81 | 137.12 | H-Bond (Protein Donor) |
| O1N | CZ | ARG- 80 | 3.89 | 0 | Ionic (Protein Cationic) |
| C3D | CG | ARG- 80 | 3.94 | 0 | Hydrophobic |
| C5D | CB | ARG- 80 | 4.22 | 0 | Hydrophobic |
| O2D | OE2 | GLU- 103 | 3.09 | 154.87 | H-Bond (Ligand Donor) |
| N1A | OH | TYR- 123 | 2.58 | 168.8 | H-Bond (Protein Donor) |
| C3N | CB | PHE- 138 | 4.37 | 0 | Hydrophobic |
| O3D | N | ASN- 140 | 3.19 | 172.88 | H-Bond (Protein Donor) |
| O2D | ND2 | ASN- 140 | 3.19 | 150.75 | H-Bond (Protein Donor) |
| O1N | CZ | ARG- 289 | 3.39 | 0 | Ionic (Protein Cationic) |
| O1N | NH1 | ARG- 289 | 3.13 | 136.76 | H-Bond (Protein Donor) |
| O1N | NH2 | ARG- 289 | 2.79 | 155.8 | H-Bond (Protein Donor) |
| C4N | CB | TYR- 294 | 3.95 | 0 | Hydrophobic |
