sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.940 Å
X-ray
2011-08-16
| Name: | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase |
|---|---|
| ID: | BIOA_MYCTU |
| AC: | P9WQ81 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 2.6.1.62 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 17 % |
| B | 83 % |
| B-Factor: | 18.922 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.949 | 745.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.01 | 42.99 |
| According to VolSite | |
| HET Code: | PL8 |
|---|---|
| Formula: | C16H20N3O7P |
| Molecular weight: | 397.320 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.55 % |
| Polar Surface area: | 176.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 39.1348 | 7.27774 | -22.7831 |
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 |
| CAL | CE2 | TRP- 64 | 4.04 | 0 | Hydrophobic |
| OAF | N | GLY- 124 | 3.07 | 147.71 | H-Bond (Protein Donor) |
| OAC | N | SER- 125 | 2.81 | 154.18 | H-Bond (Protein Donor) |
| OAC | OG | SER- 125 | 2.62 | 152.29 | H-Bond (Protein Donor) |
| CAN | CE2 | TYR- 157 | 4.06 | 0 | Hydrophobic |
| CAO | CE2 | TYR- 157 | 4.28 | 0 | Hydrophobic |
| CAA | CG | GLU- 220 | 4.18 | 0 | Hydrophobic |
| CAM | CB | ALA- 226 | 4.38 | 0 | Hydrophobic |
| NAR | OD1 | ASP- 254 | 3.48 | 121.39 | H-Bond (Ligand Donor) |
| NAR | OD2 | ASP- 254 | 2.72 | 168.3 | H-Bond (Ligand Donor) |
| CAA | CB | ILE- 256 | 4.08 | 0 | Hydrophobic |
| CAW | CG2 | ILE- 256 | 3.84 | 0 | Hydrophobic |
| CAA | CB | ALA- 257 | 4.3 | 0 | Hydrophobic |
| OAG | N | THR- 318 | 2.82 | 172.48 | H-Bond (Protein Donor) |
| OAG | OG1 | THR- 318 | 3.24 | 162.2 | H-Bond (Protein Donor) |
| CAK | CE2 | PHE- 402 | 4.11 | 0 | Hydrophobic |
| OAE | O | HOH- 563 | 3.03 | 179.98 | H-Bond (Protein Donor) |
