sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2006-12-19
| Name: | Lipoyltransferase 1, mitochondrial |
|---|---|
| ID: | LIPT_BOVIN |
| AC: | O46419 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | 2.3.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 35.422 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.958 | 361.125 |
| % Hydrophobic | % Polar |
|---|---|
| 52.34 | 47.66 |
| According to VolSite | |
| HET Code: | LAQ |
|---|---|
| Formula: | C18H25N5O8PS2 |
| Molecular weight: | 534.524 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 80.65 % |
| Polar Surface area: | 255.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 42.874 | 27.7476 | 7.08276 |
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 |
| S17 | CH2 | TRP- 40 | 3.83 | 0 | Hydrophobic |
| C17 | CZ2 | TRP- 40 | 3.65 | 0 | Hydrophobic |
| S15 | CG1 | VAL- 47 | 4.06 | 0 | Hydrophobic |
| S17 | CG1 | VAL- 47 | 4.18 | 0 | Hydrophobic |
| S17 | CD | ARG- 73 | 3.87 | 0 | Hydrophobic |
| S15 | CD | ARG- 73 | 3.65 | 0 | Hydrophobic |
| S15 | CG2 | VAL- 80 | 3.53 | 0 | Hydrophobic |
| C5' | CG1 | VAL- 80 | 4.35 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 80 | 3.75 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 80 | 4.13 | 0 | Hydrophobic |
| N7 | N | TYR- 81 | 3.04 | 167.02 | H-Bond (Protein Donor) |
| N6 | O | TYR- 81 | 3 | 159.17 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASN- 86 | 3.3 | 160.53 | H-Bond (Ligand Donor) |
| C17 | CB | ASN- 88 | 4.41 | 0 | Hydrophobic |
| O1P | CZ | ARG- 125 | 3.36 | 0 | Ionic (Protein Cationic) |
| O1P | NH1 | ARG- 125 | 2.91 | 145.18 | H-Bond (Protein Donor) |
| O1P | NH2 | ARG- 125 | 2.95 | 142.95 | H-Bond (Protein Donor) |
| O1P | NZ | LYS- 135 | 3.24 | 0 | Ionic (Protein Cationic) |
| O10 | NZ | LYS- 135 | 2.85 | 152.92 | H-Bond (Protein Donor) |
| C1' | CD | LYS- 135 | 4.42 | 0 | Hydrophobic |
| C13 | CB | ALA- 140 | 4.15 | 0 | Hydrophobic |
| C17 | CB | HIS- 151 | 3.97 | 0 | Hydrophobic |
| N1 | OG1 | THR- 153 | 2.74 | 179.22 | H-Bond (Protein Donor) |
| C16 | CG2 | THR- 153 | 3.89 | 0 | Hydrophobic |
| C2' | CD2 | LEU- 163 | 4.33 | 0 | Hydrophobic |
| C3' | CD1 | LEU- 167 | 4 | 0 | Hydrophobic |
| O2P | N | THR- 182 | 2.78 | 160.55 | H-Bond (Protein Donor) |
| O2' | O | ALA- 184 | 3.01 | 122.31 | H-Bond (Ligand Donor) |
| O2' | N | ALA- 184 | 2.89 | 143.76 | H-Bond (Protein Donor) |
| C1' | CG1 | VAL- 186 | 3.48 | 0 | Hydrophobic |
