sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.960 Å
X-ray
2012-10-02
| Name: | Cyclin-dependent kinase 9 |
|---|---|
| ID: | CDK9_HUMAN |
| AC: | P50750 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.22 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 80.489 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.991 | 627.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.99 | 43.01 |
| According to VolSite | |
| HET Code: | T7Z |
|---|---|
| Formula: | C21H23N7O3S2 |
| Molecular weight: | 485.582 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.11 % |
| Polar Surface area: | 166.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 55.1132 | -18.1395 | -12.1054 |
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 |
| C13 | CD1 | ILE- 25 | 3.83 | 0 | Hydrophobic |
| C01 | CD1 | PHE- 30 | 4.47 | 0 | Hydrophobic |
| C18 | CZ | PHE- 30 | 4.06 | 0 | Hydrophobic |
| C20 | CZ | PHE- 30 | 4.45 | 0 | Hydrophobic |
| C06 | CB | VAL- 33 | 4.48 | 0 | Hydrophobic |
| C06 | CB | ALA- 46 | 3.76 | 0 | Hydrophobic |
| C30 | CB | ALA- 46 | 3.83 | 0 | Hydrophobic |
| C06 | CD1 | PHE- 103 | 3.58 | 0 | Hydrophobic |
| N11 | O | CYS- 106 | 2.68 | 126.98 | H-Bond (Ligand Donor) |
| N28 | N | CYS- 106 | 2.94 | 151.82 | H-Bond (Protein Donor) |
| C18 | CB | ALA- 153 | 3.96 | 0 | Hydrophobic |
| C30 | CD1 | LEU- 156 | 3.35 | 0 | Hydrophobic |
| C01 | CB | ASP- 167 | 3.36 | 0 | Hydrophobic |
