MolNFT v1 · #151548 · protein
Crystal structure of protac 2 in complex with the bromodomain of human SMARCA4 and PVHL:ELONGINC:ELONGINB
6HR2 · Transcription activator BRG1: “Crystal structure of protac 2 in complex with the bromodomain of human SMARCA4 and PVHL:ELONGINC:ELONGINB”. X-ray diffraction, 1 ligand (FWZ), 9 pockets (best druggability 0.67). MolNFT v1 #151548 on…
- PDB
- 6HR2
- Type
- protein
- Length
- 916 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription activator BRG1; Von hippel-lindau disease tumor suppressor; Elongin-C…
- EC
- 3.6.4.-
- UniProt
- P51532, P40337, Q15369, Q15370
- Ligands
- FWZ
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription activator BRG1 (EC 3.6.4.-) | protein | 117 | 65% helix, 2% strand | P51532 |
| B, F | Von hippel-lindau disease tumor suppressor | protein | 149 | 25% helix, 28% strand | P40337 |
| C, G | Elongin-C | protein | 87 | 45% helix, 15% strand | Q15369 |
| D | Elongin-B | protein | 104 | 14% helix, 38% strand | Q15370 |
| E | Transcription activator BRG1 (EC 3.6.4.-) | protein | 120 | 63% helix, 2% strand | P51532 |
| H | Elongin-B | protein | 103 | 15% helix, 39% strand | Q15370 |
Ligands and binding sites
- FWZ · (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 2 copies · chains A, B, E, F
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B, E, F
- EDO · 1,2-ethanediol · additive · 2 copies · chains F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.67 | 0.78 | 48 | FWZ, DMS |
| 2 | 430 | 0.65 | 0.78 | 45 | DMS, FWZ |
| 3 | 308 | 0.61 | 0.78 | 51 | empty |
| 4 | 274 | 0.57 | 0.77 | 47 | EDO |
| 5 | 203 | 0.46 | 0.74 | 31 | empty |
Interfaces
13 interfaces between chains.
- G–H · 1157 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1156 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1107 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1093 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 931 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6HR2 · Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and… · 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 H against A, TM-score 0.98
- 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 P51532
- Every structure of UniProt P40337
- Every structure of UniProt Q15369
- Every structure of UniProt Q15370
- Elsewhere: RCSB PDB 6HR2 · PDBe 6HR2 · UniProt P51532 · UniProt P40337 · UniProt Q15369 · UniProt Q15370
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