sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2007-12-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.190 | 8.300 | 8.190 | 0.160 | 8.520 | 3 |
| 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: | 80.299 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.153 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 63.72 | 36.28 |
| According to VolSite | |
| HET Code: | CPB |
|---|---|
| Formula: | C21H20ClNO5 |
| Molecular weight: | 401.840 g/mol |
| DrugBank ID: | DB03496 |
| Buried Surface Area: | 69.57 % |
| Polar Surface area: | 94.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 53.0279 | -17.2318 | -12.7433 |
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 |
| C21 | CD1 | ILE- 25 | 3.46 | 0 | Hydrophobic |
| C13 | CD2 | PHE- 30 | 4.24 | 0 | Hydrophobic |
| CL1 | CZ | PHE- 30 | 4.49 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 33 | 3.85 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 33 | 4.07 | 0 | Hydrophobic |
| C5 | CB | ALA- 46 | 3.94 | 0 | Hydrophobic |
| C13 | CD | LYS- 48 | 4.46 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 79 | 3.94 | 0 | Hydrophobic |
| C5 | CB | PHE- 103 | 4.26 | 0 | Hydrophobic |
| O4 | N | CYS- 106 | 3.15 | 156.27 | H-Bond (Protein Donor) |
| C25 | CB | ASP- 109 | 4.29 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 156 | 4.38 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 156 | 4.45 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 156 | 3.23 | 0 | Hydrophobic |
| C15 | CB | ALA- 166 | 4.13 | 0 | Hydrophobic |
| C7 | CB | ALA- 166 | 4.05 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 167 | 3.27 | 140.49 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 167 | 3.27 | 0 | Ionic (Ligand Cationic) |
| C15 | CB | ASP- 167 | 3.78 | 0 | Hydrophobic |
