Research workbench
Ternary complex of VHL/BRD4-BD1/COMPOUND9 (4-(3,5-difluoropyridin-2- yl)-N-(11-(((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl) BENZYL)CARBAMOYL)PYRROLIDIN-1-yl)-3,3-dimethyl-1-oxobutan-2-yl) amino)-11-oxoundecyl)-10-methyl-7-((METHYLSULFONYL)METHYL)-11-oxo-3, 4,10,11-tetrahydro-1H-1,4,10-TRIAZADIBENZO[CD,F]AZULENE-6- carboxamide)
Analyse Ternary complex of VHL/BRD4-BD1/COMPOUND9 (4-(3,5-difluoropyridin-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KHH
- Type
- protein
- Length
- 471 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongin-B; Elongin-C; Von hippel-lindau disease tumor suppressor; Bromodomain-containing…
- UniProt
- Q15370, Q15369, P40337, O60885
- Ligands
- WEP
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongin-B | protein | 105 | 20% helix, 38% strand | Q15370 |
| B | Elongin-C | protein | 90 | 43% helix, 14% strand | Q15369 |
| C | Von hippel-lindau disease tumor suppressor | protein | 148 | 28% helix, 28% strand | P40337 |
| D | Bromodomain-containing protein 4 | protein | 128 | 55% helix, 0% strand | O60885 |
Ligands and binding sites
- WEP · N-[11-({7-(3,5-difluoropyridin-2-yl)-2-methyl-10-[(methylsulfonyl)methyl]-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[cd,f]azulene-9-carbonyl}amino) undecanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide · ligand · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.68 | 0.77 | 40 | WEP |
| 2 | 179 | 0.46 | 0.75 | 34 | empty |
| 3 | 55 | 0.27 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1165 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1087 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 377 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 210 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 7KHH · Ternary complex of VHL/BRD4-BD1/Compound9 (4-(3,5-difluoropyridin-2-yl)-N-(11-(((S)-1-((2S… · the same entry in another collection · chain A against A, TM-score 1.00
- Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · 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 D against A, TM-score 0.98
- Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q15370
- Every structure of UniProt Q15369
- Every structure of UniProt P40337
- Every structure of UniProt O60885
- Elsewhere: RCSB PDB 7KHH · PDBe 7KHH · UniProt Q15370 · UniProt Q15369 · UniProt P40337 · UniProt O60885
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