sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.680 Å
X-ray
2011-12-08
| Name: | Histo-blood group ABO system transferase |
|---|---|
| ID: | BGAT_HUMAN |
| AC: | P16442 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 26.477 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.432 | 550.125 |
| % Hydrophobic | % Polar |
|---|---|
| 47.85 | 52.15 |
| According to VolSite | |
| HET Code: | 5GW |
|---|---|
| Formula: | C15H15N2O12P2 |
| Molecular weight: | 477.233 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.83 % |
| Polar Surface area: | 240.5 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 17.3214 | -1.5089 | 34.431 |
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 |
| OAI | MN | MN- 1 | 2.21 | 0 | Metal Acceptor |
| OAG | MN | MN- 1 | 2.11 | 0 | Metal Acceptor |
| C1' | CB | PHE- 121 | 4.36 | 0 | Hydrophobic |
| O2' | O | PHE- 121 | 2.65 | 177.05 | H-Bond (Ligand Donor) |
| NAQ | O | ILE- 123 | 2.91 | 151.24 | H-Bond (Ligand Donor) |
| OAB | N | ILE- 123 | 2.79 | 161.65 | H-Bond (Protein Donor) |
| C3' | CE1 | TYR- 126 | 3.71 | 0 | Hydrophobic |
| CAM | CE2 | TYR- 126 | 3.13 | 0 | Hydrophobic |
| C2' | CD1 | TYR- 126 | 3.62 | 0 | Hydrophobic |
| OAD | OH | TYR- 126 | 2.62 | 130.98 | H-Bond (Protein Donor) |
| CAL | CE3 | TRP- 181 | 2.99 | 0 | Hydrophobic |
| CAK | CB | TRP- 181 | 3.26 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 184 | 4.33 | 0 | Hydrophobic |
| C5' | CB | SER- 185 | 4.46 | 0 | Hydrophobic |
| C3' | CB | ASP- 211 | 4.46 | 0 | Hydrophobic |
| O2' | N | VAL- 212 | 3.42 | 139.65 | H-Bond (Protein Donor) |
| O3' | N | VAL- 212 | 3.01 | 151.71 | H-Bond (Protein Donor) |
| C2' | CG1 | VAL- 212 | 3.55 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 213 | 2.92 | 133.98 | H-Bond (Ligand Donor) |
| OAI | NZ | LYS- 346 | 3.99 | 0 | Ionic (Protein Cationic) |
| OAD | NZ | LYS- 346 | 3.89 | 0 | Ionic (Protein Cationic) |
| OAG | NZ | LYS- 346 | 3.81 | 0 | Ionic (Protein Cationic) |
| OAH | NZ | LYS- 346 | 2.96 | 0 | Ionic (Protein Cationic) |
| OAH | NZ | LYS- 346 | 2.96 | 168.47 | H-Bond (Protein Donor) |
| O2' | O | HOH- 409 | 2.77 | 150.83 | H-Bond (Protein Donor) |
