MolNFT v1 · #106895 · protein
Crystal structure of a CDK6/VCYCLIN complex with inhibitor bound
4TTH · Cyclin homolog: “Crystal structure of a CDK6/VCYCLIN complex with inhibitor bound”. X-ray diffraction, 1 ligand (24V), 6 pockets (best druggability 0.69). MolNFT v1 #106895 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4TTH
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin homolog; Cyclin-dependent kinase 6
- EC
- 2.7.11.22
- UniProt
- Q01043, Q00534
- Ligands
- 24V
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin homolog | protein | 244 | 67% helix, 0% strand | Q01043 |
| B | Cyclin-dependent kinase 6 (EC 2.7.11.22) | protein | 256 | 33% helix, 13% strand | Q00534 |
Ligands and binding sites
- 24V · 9-cyclopentyl-N-(5-piperazin-1-ylpyridin-2-yl)pyrido[4,5]pyrrolo[1,2-d]pyrimidin-2-amine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.69 | 0.86 | 36 | empty |
| 2 | 205 | 0.64 | 0.83 | 25 | 24V |
| 3 | 108 | 0.55 | 0.83 | 27 | empty |
| 4 | 58 | 0.50 | 0.85 | 16 | empty |
| 5 | 97 | 0.48 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2148 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4TTH · Crystal structure of a CDK6/Vcyclin complex with inhibitor bound · the same entry in another collection · chain A against A, TM-score 1.00
- Q00534 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 6 (Q00534) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q01043
- Every structure of UniProt Q00534
- Elsewhere: RCSB PDB 4TTH · PDBe 4TTH · UniProt Q01043 · UniProt Q00534
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