sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2010-10-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.000 | 5.120 | 5.070 | 0.130 | 5.300 | 3 |
| Name: | Lethal(3)malignant brain tumor-like protein 1 |
|---|---|
| ID: | LMBL1_HUMAN |
| AC: | Q9Y468 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 76 % |
| B | 24 % |
| B-Factor: | 38.409 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.164 | 1306.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.83 | 59.17 |
| According to VolSite | |
| HET Code: | P8H |
|---|---|
| Formula: | C15H21BrN3O |
| Molecular weight: | 339.251 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.33 % |
| Polar Surface area: | 37.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 22.247 | 28.8476 | -13.6957 |
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 |
| N16 | OD2 | ASP- 355 | 2.62 | 167.86 | H-Bond (Ligand Donor) |
| N16 | OD2 | ASP- 355 | 2.62 | 0 | Ionic (Ligand Cationic) |
| C18 | CB | ASP- 355 | 4.09 | 0 | Hydrophobic |
| C6 | CB | ASN- 358 | 3.92 | 0 | Hydrophobic |
| BR8 | CB | ASN- 358 | 4.33 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 361 | 3.43 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 361 | 3.87 | 0 | Hydrophobic |
| C18 | SG | CYS- 363 | 3.56 | 0 | Hydrophobic |
| C19 | CG | PHE- 379 | 3.56 | 0 | Hydrophobic |
| C12 | CH2 | TRP- 382 | 4.43 | 0 | Hydrophobic |
| C14 | CZ3 | TRP- 382 | 3.9 | 0 | Hydrophobic |
| C18 | CE2 | TRP- 382 | 4.15 | 0 | Hydrophobic |
| C19 | CB | TRP- 382 | 4.17 | 0 | Hydrophobic |
| C14 | CZ | TYR- 386 | 3.44 | 0 | Hydrophobic |
| C19 | CG | TYR- 386 | 3.71 | 0 | Hydrophobic |
