sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2009-06-30
| Name: | NmrA-like family domain-containing protein 1 |
|---|---|
| ID: | NMRL1_HUMAN |
| AC: | Q9HBL8 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 14.427 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.876 | 286.875 |
| % Hydrophobic | % Polar |
|---|---|
| 63.53 | 36.47 |
| According to VolSite | |
| HET Code: | ZZ0 |
|---|---|
| Formula: | C12H8ClN2O2 |
| Molecular weight: | 247.657 g/mol |
| DrugBank ID: | DB08784 |
| Buried Surface Area: | 69 % |
| Polar Surface area: | 65.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -23.439 | 9.69624 | -2.35576 |
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 |
| O2 | NE1 | TRP- 82 | 2.81 | 154 | H-Bond (Protein Donor) |
| C12 | CB | CYS- 154 | 4.05 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 162 | 3.78 | 0 | Aromatic Face/Face |
| C5 | CB | HIS- 162 | 3.7 | 0 | Hydrophobic |
| C10 | CB | HIS- 162 | 3.6 | 0 | Hydrophobic |
| CL1 | CE1 | PHE- 251 | 4.09 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 257 | 4.42 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 257 | 4.49 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 257 | 3.89 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 257 | 3.56 | 0 | Hydrophobic |
| C12 | SD | MET- 260 | 3.35 | 0 | Hydrophobic |
| O1 | O2D | NAP- 1300 | 2.68 | 162.4 | H-Bond (Protein Donor) |
