Research workbench
Crystal structure of DDB1-crbn-BRD4(BD1) complex bound to DBET6 protac.
Analyse Crystal structure of DDB1-crbn-BRD4(BD1) complex bound to DBET6 protac. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BOY
- Type
- protein
- Length
- 1,310 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; Protein cereblon; Bromodomain-containing protein 4
- UniProt
- Q16531, Q96SW2, O60885
- Ligands
- RN6, ZN
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 808 | 8% helix, 50% strand | Q16531 |
| B | Protein cereblon | protein | 375 | 26% helix, 33% strand | Q96SW2 |
| C | Bromodomain-containing protein 4 | protein | 127 | 52% helix, 0% strand | O60885 |
Ligands and binding sites
- RN6 · 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3, 2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl) acetamide · ligand · chains B, C
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.87 | 0.88 | 86 | empty |
| 2 | 1026 | 0.83 | 0.84 | 98 | empty |
| 3 | 562 | 0.73 | 0.81 | 40 | empty |
| 4 | 758 | 0.70 | 0.77 | 73 | empty |
| 5 | 390 | 0.62 | 0.77 | 45 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2355 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 595 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6BOY · Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC. · the same entry in another collection · chain A against A, TM-score 1.00
- Q96SW2 · AlphaFold monomer V2.0 prediction for protein cereblon (Q96SW2) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q16531
- Every structure of UniProt Q96SW2
- Every structure of UniProt O60885
- Elsewhere: RCSB PDB 6BOY · PDBe 6BOY · UniProt Q16531 · UniProt Q96SW2 · UniProt O60885
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