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
2011-07-21
| Name: | Transporter |
|---|---|
| ID: | Q9K0A9_NEIMB |
| AC: | Q9K0A9 |
| Organism: | Neisseria meningitidis serogroup B |
| Reign: | Bacteria |
| TaxID: | 122586 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 62.475 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.623 | 914.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.40 | 47.60 |
| According to VolSite | |
| HET Code: | TCH |
|---|---|
| Formula: | C26H44NO7S |
| Molecular weight: | 514.695 g/mol |
| DrugBank ID: | DB04348 |
| Buried Surface Area: | 43.99 % |
| Polar Surface area: | 155.37 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 24.8331 | 75.7463 | 73.1338 |
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 |
| O1S | NZ | LYS- 13 | 3.33 | 142.36 | H-Bond (Protein Donor) |
| O1S | NZ | LYS- 13 | 3.33 | 0 | Ionic (Protein Cationic) |
| C23 | CG | LYS- 13 | 3.75 | 0 | Hydrophobic |
| C26 | CG | LYS- 13 | 3.58 | 0 | Hydrophobic |
| C6 | CZ | PHE- 15 | 3.42 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 15 | 3.41 | 0 | Hydrophobic |
| C15 | CD2 | PHE- 15 | 3.6 | 0 | Hydrophobic |
| C16 | CB | PHE- 15 | 4.42 | 0 | Hydrophobic |
| C18 | CB | PHE- 15 | 4.05 | 0 | Hydrophobic |
| C8 | CD2 | PHE- 15 | 4.15 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 47 | 3.55 | 0 | Hydrophobic |
| O3 | OG1 | THR- 112 | 2.73 | 154.67 | H-Bond (Ligand Donor) |
| C14 | CB | ALA- 113 | 4.05 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 116 | 3.61 | 0 | Hydrophobic |
| C16 | CE | MET- 117 | 4.48 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 120 | 4.48 | 0 | Hydrophobic |
| C1 | CB | SER- 199 | 3.53 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 200 | 4.04 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 200 | 3.59 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 203 | 3.71 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 203 | 3.7 | 0 | Hydrophobic |
| O7 | OD1 | ASN- 295 | 3.03 | 165.61 | H-Bond (Ligand Donor) |
| O7 | ND2 | ASN- 295 | 3.25 | 135.93 | H-Bond (Protein Donor) |
| O7 | O | HOH- 2024 | 3.04 | 169.05 | H-Bond (Protein Donor) |
