sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.950 Å
X-ray
2011-09-01
| 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: | 89.183 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.739 | 367.875 |
| % Hydrophobic | % Polar |
|---|---|
| 55.96 | 44.04 |
| According to VolSite | |
| HET Code: | F18 |
|---|---|
| Formula: | C9H10N6O |
| Molecular weight: | 218.215 g/mol |
| DrugBank ID: | DB07731 |
| Buried Surface Area: | 63.77 % |
| Polar Surface area: | 125.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 51.5596 | -14.6833 | -13.6363 |
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 | O | ILE- 25 | 3.06 | 122.77 | H-Bond (Ligand Donor) |
| O3 | NZ | LYS- 48 | 3.43 | 120.76 | H-Bond (Protein Donor) |
| C1 | CD | LYS- 48 | 4.43 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 79 | 4.25 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 79 | 3.9 | 0 | Hydrophobic |
| C6 | CZ | PHE- 103 | 3.23 | 0 | Hydrophobic |
| N18 | O | ASP- 104 | 3.36 | 158.18 | H-Bond (Ligand Donor) |
| N17 | N | CYS- 106 | 3.18 | 153.33 | H-Bond (Protein Donor) |
| C2 | CB | ALA- 166 | 4.02 | 0 | Hydrophobic |
| C1 | CB | ASP- 167 | 4 | 0 | Hydrophobic |
| O3 | N | PHE- 168 | 3.34 | 132.62 | H-Bond (Protein Donor) |
