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
2013-04-10
| Name: | N-acetylglutamate synthase, mitochondrial |
|---|---|
| ID: | NAGS_HUMAN |
| AC: | Q8N159 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.3.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| Y | 100 % |
| B-Factor: | 71.385 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.721 | 570.375 |
| % Hydrophobic | % Polar |
|---|---|
| 44.97 | 55.03 |
| According to VolSite | |
| HET Code: | NLG |
|---|---|
| Formula: | C7H9NO5 |
| Molecular weight: | 187.150 g/mol |
| DrugBank ID: | DB04075 |
| Buried Surface Area: | 74.13 % |
| Polar Surface area: | 109.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 14.6373 | 107.888 | 110.712 |
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 |
| CB | CZ | PHE- 399 | 3.86 | 0 | Hydrophobic |
| CG | CE1 | PHE- 399 | 3.53 | 0 | Hydrophobic |
| OE2 | NZ | LYS- 401 | 3.31 | 156.4 | H-Bond (Protein Donor) |
| OE2 | NZ | LYS- 401 | 3.31 | 0 | Ionic (Protein Cationic) |
| C8 | CG | LEU- 442 | 4.13 | 0 | Hydrophobic |
| OXT | NZ | LYS- 444 | 2.67 | 134.78 | H-Bond (Protein Donor) |
| OXT | NZ | LYS- 444 | 2.67 | 0 | Ionic (Protein Cationic) |
| C8 | CB | PHE- 445 | 4.4 | 0 | Hydrophobic |
| O7 | N | PHE- 445 | 3 | 149.7 | H-Bond (Protein Donor) |
| C8 | CB | TRP- 473 | 3.83 | 0 | Hydrophobic |
| O | CZ | ARG- 474 | 4 | 0 | Ionic (Protein Cationic) |
| O | NE | ARG- 474 | 3.16 | 175.59 | H-Bond (Protein Donor) |
| OE1 | N | ARG- 476 | 3.1 | 175.06 | H-Bond (Protein Donor) |
| OE1 | ND2 | ASN- 479 | 3.48 | 164.89 | H-Bond (Protein Donor) |
| CG | CZ3 | TRP- 498 | 4.18 | 0 | Hydrophobic |
| CG | CE1 | PHE- 525 | 4.39 | 0 | Hydrophobic |
