MolNFT v1 · #113333 · protein
Crystal structure of the human CDK12-cyclink complex
5ACB · Cyclin-K: “Crystal structure of the human CDK12-cyclink complex”. X-ray diffraction, 1 ligand (5I1), 15 pockets (best druggability 0.64). MolNFT v1 #113333 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ACB
- Type
- protein
- Length
- 1,130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-K; Cyclin-dependent kinase 12
- EC
- 2.7.11.22
- UniProt
- G3V5E1, Q9NYV4
- Ligands
- 5I1
- Pockets
- 15 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-K | protein | 237 | 68% helix, 0% strand | G3V5E1 |
| B | Cyclin-K | protein | 248 | 65% helix, 0% strand | G3V5E1 |
| C | Cyclin-dependent kinase 12 (EC 2.7.11.22) | protein | 325 | 33% helix, 16% strand | Q9NYV4 |
| D | Cyclin-dependent kinase 12 (EC 2.7.11.22) | protein | 320 | 34% helix, 16% strand | Q9NYV4 |
Ligands and binding sites
- 5I1 · N-[4-[(3R)-3-[[5-chloranyl-4-(1H-indol-3-yl)pyrimidin-2-yl]amino]piperidin-1-yl]carbonylphenyl]-4-(dimethylamino)butanamide · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.64 | 0.79 | 45 | 5I1 |
| 2 | 317 | 0.64 | 0.80 | 39 | 5I1 |
| 3 | 75 | 0.54 | 0.86 | 21 | empty |
| 4 | 168 | 0.53 | 0.79 | 28 | empty |
| 5 | 180 | 0.51 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1321 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1208 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
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 G3V5E1
- Every structure of UniProt Q9NYV4
- Elsewhere: RCSB PDB 5ACB · PDBe 5ACB · UniProt G3V5E1 · UniProt Q9NYV4
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