sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.730 Å
X-ray
2013-11-25
| Name: | Bromodomain-containing protein 9 |
|---|---|
| ID: | BRD9_HUMAN |
| AC: | Q9H8M2 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.381 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.944 | 253.125 |
| % Hydrophobic | % Polar |
|---|---|
| 65.33 | 34.67 |
| According to VolSite | |
| HET Code: | Y1Z |
|---|---|
| Formula: | C26H23ClN6O3S |
| Molecular weight: | 535.017 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 42.54 % |
| Polar Surface area: | 110.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -13.2435 | 15.608 | -13.607 |
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 |
| CAW | CD1 | PHE- 44 | 4.39 | 0 | Hydrophobic |
| CAN | CB | PHE- 44 | 4.28 | 0 | Hydrophobic |
| CAT | CD1 | PHE- 44 | 3.42 | 0 | Hydrophobic |
| CAO | CB | PHE- 44 | 4.29 | 0 | Hydrophobic |
| CAN | CE1 | PHE- 45 | 3.54 | 0 | Hydrophobic |
| CAN | CG2 | VAL- 49 | 3.84 | 0 | Hydrophobic |
| CBA | CD1 | ILE- 53 | 4.22 | 0 | Hydrophobic |
| CAQ | CD1 | ILE- 53 | 4.16 | 0 | Hydrophobic |
| CAO | CG2 | ILE- 53 | 3.75 | 0 | Hydrophobic |
| CAC | CG2 | ILE- 53 | 3.29 | 0 | Hydrophobic |
| CBH | CG2 | ILE- 53 | 3.92 | 0 | Hydrophobic |
| CAF | CB | ALA- 54 | 3.94 | 0 | Hydrophobic |
| NAM | ND2 | ASN- 100 | 2.88 | 173.11 | H-Bond (Protein Donor) |
| NAL | ND2 | ASN- 100 | 3.47 | 143.94 | H-Bond (Protein Donor) |
| OBC | OH | TYR- 106 | 2.95 | 139.24 | H-Bond (Protein Donor) |
| CAE | CB | TYR- 106 | 4.5 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 106 | 3.7 | 0 | Aromatic Face/Face |
