sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2009-03-10
| Name: | Niemann-Pick C1 protein |
|---|---|
| ID: | NPC1_HUMAN |
| AC: | O15118 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 23.360 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.611 | 661.500 |
| % Hydrophobic | % Polar |
|---|---|
| 58.67 | 41.33 |
| According to VolSite | |
| HET Code: | HC3 |
|---|---|
| Formula: | C27H46O2 |
| Molecular weight: | 402.653 g/mol |
| DrugBank ID: | DB04705 |
| Buried Surface Area: | 75.2 % |
| Polar Surface area: | 40.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -35.9344 | -27.7283 | 2.60083 |
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 |
| O1 | O | HOH- 4 | 2.77 | 151.84 | H-Bond (Ligand Donor) |
| C4 | CH2 | TRP- 27 | 4.3 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 41 | 2.97 | 144.67 | H-Bond (Protein Donor) |
| O1 | NE2 | GLN- 79 | 3 | 166.77 | H-Bond (Protein Donor) |
| C19 | CG2 | THR- 82 | 3.87 | 0 | Hydrophobic |
| C2 | CG2 | THR- 82 | 3.99 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 83 | 3.96 | 0 | Hydrophobic |
| C1 | CB | LEU- 83 | 3.83 | 0 | Hydrophobic |
| C18 | CB | ASN- 86 | 4.22 | 0 | Hydrophobic |
| C21 | CB | ASN- 86 | 4.49 | 0 | Hydrophobic |
| C11 | CB | ASN- 86 | 3.53 | 0 | Hydrophobic |
| C21 | CG | PRO- 90 | 3.55 | 0 | Hydrophobic |
| C22 | CG | PRO- 90 | 4.1 | 0 | Hydrophobic |
| C7 | CD1 | PHE- 108 | 4.48 | 0 | Hydrophobic |
| C14 | CE1 | PHE- 108 | 3.58 | 0 | Hydrophobic |
| C17 | CZ | PHE- 108 | 3.55 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 111 | 3.74 | 0 | Hydrophobic |
| C3 | CG2 | THR- 112 | 3.56 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 176 | 4.42 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 176 | 3.49 | 0 | Hydrophobic |
| C27 | CE2 | TYR- 192 | 3.67 | 0 | Hydrophobic |
| C16 | CB | MET- 193 | 4.13 | 0 | Hydrophobic |
| C22 | SD | MET- 193 | 3.86 | 0 | Hydrophobic |
| C27 | CG | MET- 193 | 4.24 | 0 | Hydrophobic |
| C23 | CG | MET- 193 | 4.03 | 0 | Hydrophobic |
| C15 | CD1 | PHE- 194 | 4.04 | 0 | Hydrophobic |
| C26 | CB | ASN- 198 | 3.95 | 0 | Hydrophobic |
| C18 | CG | GLN- 200 | 3.95 | 0 | Hydrophobic |
| C20 | CG | GLN- 200 | 4.16 | 0 | Hydrophobic |
| C26 | CB | GLN- 200 | 3.86 | 0 | Hydrophobic |
| C15 | CB | ALA- 201 | 4.12 | 0 | Hydrophobic |
| C19 | CG | PRO- 202 | 3.69 | 0 | Hydrophobic |
| C4 | CZ | PHE- 203 | 3.77 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 205 | 3.85 | 0 | Hydrophobic |
