MolNFT v1 · #143566 · protein
Crystal structure of human CDK12/CYCLINK in complex with an inhibitor
6B3E · Cyclin-dependent kinase 12: “Crystal structure of human CDK12/CYCLINK in complex with an inhibitor”. X-ray diffraction, 2 ligands (CJM, MG), 15 pockets (best druggability 0.74). MolNFT v1 #143566 on GenesisL1: 3D structure, binding…
- PDB
- 6B3E
- Type
- protein
- Length
- 1,099 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
- CJM, MG
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 48% 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 | 310 | 34% helix, 15% strand | Q9NYV4 |
| B | Cyclin-K | protein | 240 | 66% helix, 0% strand | O75909 |
| C | Cyclin-dependent kinase 12 (EC 2.7.11.22, 2.7.11.23) | protein | 308 | 34% helix, 16% strand | Q9NYV4 |
| D | Cyclin-K | protein | 241 | 66% helix, 0% strand | O75909 |
Ligands and binding sites
- CJM · 2-[(2S)-1-(6-{[(4,5-difluoro-1H-benzimidazol-2-yl) methyl]amino}-9-ethyl-9H-purin-2-yl)piperidin-2-yl]ethan-1-ol · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.74 | 0.77 | 113 | empty |
| 2 | 287 | 0.66 | 0.82 | 31 | MG, CJM |
| 3 | 416 | 0.65 | 0.79 | 52 | empty |
| 4 | 211 | 0.64 | 0.83 | 26 | EDO, CJM |
| 5 | 473 | 0.62 | 0.76 | 53 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 1106 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 952 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 556 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 555 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6B3E · Crystal structure of human CDK12/CyclinK in complex with an inhibitor · the same entry in another collection · chain D against D, 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 A against A, TM-score 0.99
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 6B3E · PDBe 6B3E · UniProt Q9NYV4 · UniProt O75909
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.