sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2010-12-17
| Name: | D-alanine--D-alanine ligase A |
|---|---|
| ID: | DDLA_SALTY |
| AC: | P0A1F0 |
| Organism: | Salmonella typhimurium |
| Reign: | Bacteria |
| TaxID: | 99287 |
| EC Number: | 6.3.2.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 50.577 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.076 | 1366.875 |
| % Hydrophobic | % Polar |
|---|---|
| 39.01 | 60.99 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.47 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 51.6117 | 14.9229 | 53.9558 |
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 | NZ | LYS- 141 | 3.2 | 147.52 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 141 | 3.2 | 0 | Ionic (Protein Cationic) |
| C1' | CE1 | PHE- 183 | 3.83 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 183 | 3.61 | 0 | Aromatic Face/Face |
| O2A | NZ | LYS- 185 | 2.75 | 167.7 | H-Bond (Protein Donor) |
| N7 | NZ | LYS- 185 | 2.98 | 152.26 | H-Bond (Protein Donor) |
| O2A | NZ | LYS- 185 | 2.75 | 0 | Ionic (Protein Cationic) |
| C5' | CB | SER- 192 | 4.26 | 0 | Hydrophobic |
| N6 | OE1 | GLU- 221 | 2.81 | 161.51 | H-Bond (Ligand Donor) |
| N6 | O | GLN- 222 | 2.84 | 142.99 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 224 | 2.71 | 165.86 | H-Bond (Protein Donor) |
| O3' | OE1 | GLU- 228 | 3.03 | 146.09 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 228 | 3.09 | 150.36 | H-Bond (Ligand Donor) |
| C3' | CD1 | LEU- 249 | 4.18 | 0 | Hydrophobic |
| C2' | CE1 | PHE- 304 | 4.15 | 0 | Hydrophobic |
| O1A | ND2 | ASN- 314 | 3.24 | 139.87 | H-Bond (Protein Donor) |
| O1B | MG | MG- 372 | 2.2 | 0 | Metal Acceptor |
| O1A | MG | MG- 372 | 2.4 | 0 | Metal Acceptor |
