MolNFT v1 · #163954 · protein
Crystal structure of macrocyclic protac 1 in complex with the second bromodomain of human BRD4 and PVHL:ELONGINC:ELONGINB
6SIS · Bromodomain-containing protein 4: “Crystal structure of macrocyclic protac 1 in complex with the second bromodomain of human BRD4 and…”. X-ray diffraction, 1 ligand (LFE), 10 pockets (best druggability 0.70). MolNFT v1 #163954 on…
- PDB
- 6SIS
- Type
- protein
- Length
- 902 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4; Elongin-B; Elongin-C; Von hippel-lindau disease tumor…
- UniProt
- O60885, Q15370, Q15369, P40337
- Ligands
- LFE
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Bromodomain-containing protein 4 | protein | 111 | 68% helix, 0% strand | O60885 |
| B, F | Elongin-B | protein | 104 | 18% helix, 35% strand | Q15370 |
| C, G | Elongin-C | protein | 87 | 48% helix, 14% strand | Q15369 |
| D, H | Von hippel-lindau disease tumor suppressor | protein | 149 | 28% helix, 27% strand | P40337 |
Ligands and binding sites
- LFE · ~{N}-[(5~{S},7~{R},11~{S},23~{S})-11-~{tert}-butyl-34-(4-methyl-1,3-thiazol-5-yl)-7-oxidanyl-4,10,13-tris(oxidanylidene)-15,18,21,25,28,31-hexaoxa-3,9,12-triazatricyclo[30.4.0.0^{5,9}]hexatriaconta-1(32),33, 35-trien-23-yl]-2-[(7~{S},9~{S})-7-(4-chlorophenyl)-4, 5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanamide · ligand · 2 copies · chains A, D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.70 | 0.78 | 53 | LFE |
| 2 | 615 | 0.70 | 0.78 | 66 | LFE |
| 3 | 157 | 0.50 | 0.78 | 26 | empty |
| 4 | 93 | 0.49 | 0.82 | 20 | empty |
| 5 | 154 | 0.48 | 0.77 | 27 | empty |
Interfaces
16 interfaces between chains.
- B–C · 1161 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1141 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1088 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1086 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 879 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6SIS · Crystal structure of macrocyclic PROTAC 1 in complex with the second bromodomain of human… · the same entry in another collection · chain H against H, TM-score 1.00
- Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain F against A, TM-score 0.99
- Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · 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 O60885
- Every structure of UniProt Q15370
- Every structure of UniProt Q15369
- Every structure of UniProt P40337
- Elsewhere: RCSB PDB 6SIS · PDBe 6SIS · UniProt O60885 · UniProt Q15370 · UniProt Q15369 · UniProt P40337
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