sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2014-06-04
| Name: | Phosphopantetheinyl transferase, PptII |
|---|---|
| ID: | A0PQD8_MYCUA |
| AC: | A0PQD8 |
| Organism: | Mycobacterium ulcerans |
| Reign: | Bacteria |
| TaxID: | 362242 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 13.692 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.750 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.92 | 57.08 |
| According to VolSite | |
| HET Code: | COA |
|---|---|
| Formula: | C21H32N7O16P3S |
| Molecular weight: | 763.502 g/mol |
| DrugBank ID: | DB01992 |
| Buried Surface Area: | 65.69 % |
| Polar Surface area: | 426.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| -11.1803 | -15.9895 | 4.60533 |
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 |
| O8A | CZ | ARG- 48 | 3.75 | 0 | Ionic (Protein Cationic) |
| O9A | CZ | ARG- 48 | 3.91 | 0 | Ionic (Protein Cationic) |
| O8A | NH2 | ARG- 48 | 3.02 | 145.13 | H-Bond (Protein Donor) |
| O9A | NH1 | ARG- 48 | 3.14 | 165.71 | H-Bond (Protein Donor) |
| O7A | NH2 | ARG- 56 | 3.5 | 127.12 | H-Bond (Protein Donor) |
| O7A | NH1 | ARG- 56 | 2.81 | 153.97 | H-Bond (Protein Donor) |
| O9A | NH1 | ARG- 56 | 3.27 | 129.74 | H-Bond (Protein Donor) |
| O7A | CZ | ARG- 56 | 3.58 | 0 | Ionic (Protein Cationic) |
| O7A | NZ | LYS- 75 | 3.67 | 0 | Ionic (Protein Cationic) |
| O8A | NZ | LYS- 75 | 2.81 | 0 | Ionic (Protein Cationic) |
| O8A | NZ | LYS- 75 | 2.81 | 140.03 | H-Bond (Protein Donor) |
| N6A | O | LYS- 78 | 3.37 | 147.31 | H-Bond (Ligand Donor) |
| O2A | OG1 | THR- 92 | 2.57 | 163.62 | H-Bond (Protein Donor) |
| O1A | ND1 | HIS- 93 | 2.77 | 145.31 | H-Bond (Protein Donor) |
| O1A | N | HIS- 93 | 3.11 | 151.52 | H-Bond (Protein Donor) |
| O4A | OD2 | ASP- 114 | 2.62 | 173.83 | H-Bond (Protein Donor) |
| S1P | CB | LYS- 156 | 3.78 | 0 | Hydrophobic |
| CEP | CB | GLU- 157 | 4.3 | 0 | Hydrophobic |
| S1P | CB | THR- 159 | 4.19 | 0 | Hydrophobic |
| CDP | CE2 | TYR- 160 | 4.36 | 0 | Hydrophobic |
| CEP | CD2 | TYR- 160 | 3.69 | 0 | Hydrophobic |
| C6P | CG | TYR- 160 | 3.63 | 0 | Hydrophobic |
| C2P | CB | TYR- 160 | 3.9 | 0 | Hydrophobic |
| O5B | NZ | LYS- 161 | 3.12 | 126.68 | H-Bond (Protein Donor) |
| O2A | NZ | LYS- 161 | 3.02 | 162.6 | H-Bond (Protein Donor) |
| O2A | NZ | LYS- 161 | 3.02 | 0 | Ionic (Protein Cationic) |
| CEP | CG | LYS- 161 | 4.24 | 0 | Hydrophobic |
| C6P | CH2 | TRP- 170 | 3.79 | 0 | Hydrophobic |
| N4P | O | LEU- 171 | 2.82 | 156.81 | H-Bond (Ligand Donor) |
| C2P | CD2 | LEU- 171 | 3.59 | 0 | Hydrophobic |
| S1P | CB | ALA- 176 | 3.77 | 0 | Hydrophobic |
| O4A | MG | MG- 302 | 2.35 | 0 | Metal Acceptor |
| O2B | O | HOH- 421 | 3.32 | 121.51 | H-Bond (Ligand Donor) |
