Research workbench
Crystal structure of human CDK12/CYCLIN K in complex with the inhibitor bsj-01-175
Analyse Crystal structure of human CDK12/CYCLIN K in complex with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NXK
- Type
- protein
- Length
- 1,123 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 12; Cyclin-K
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- Q9NYV4, O75909
- Ligands
- UUB
- Pockets
- 18 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 12 (EC 2.7.11.22, 2.7.11.23) | protein | 322 | 29% helix, 15% strand | Q9NYV4 |
| B | Cyclin-K | protein | 246 | 63% helix, 0% strand | O75909 |
| C | Cyclin-dependent kinase 12 (EC 2.7.11.22, 2.7.11.23) | protein | 314 | 31% helix, 16% strand | Q9NYV4 |
| D | Cyclin-K | protein | 241 | 65% helix, 0% strand | O75909 |
Ligands and binding sites
- UUB · (E)-N-[4-[(1R,3R)-3-[[5-chloranyl-4-(1H-indol-3-yl) pyrimidin-2-yl]amino]cyclohexyl]oxyphenyl]-4-(dimethylamino)but-2-enamide · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.69 | 0.80 | 44 | UUB |
| 2 | 419 | 0.65 | 0.78 | 43 | UUB |
| 3 | 379 | 0.65 | 0.79 | 43 | empty |
| 4 | 362 | 0.63 | 0.79 | 49 | empty |
| 5 | 322 | 0.61 | 0.78 | 36 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1227 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1002 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 492 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 475 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 7NXK · Crystal structure of human Cdk12/Cyclin K in complex with the inhibitor BSJ-01-175 · the same entry in another collection · chain A against A, TM-score 1.00
- O75909 · AlphaFold monomer V2.0 prediction for cyclin-K (O75909) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q9NYV4 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 12 (Q9NYV4) · a predicted model of the same protein · chain C against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9NYV4
- Every structure of UniProt O75909
- Elsewhere: RCSB PDB 7NXK · PDBe 7NXK · UniProt Q9NYV4 · UniProt O75909
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