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› 7z76

X-ray diffraction
1.32Å resolution

Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB

Released:
DOI: 10.2210/pdb7z76/pdb
Model geometry
Fit model/data
PDB entry 7z76 coloured by chain, front view.
PDB entry 7z76 coloured by chain, side view.
PDB entry 7z76 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo.
Kofink C, Trainor N, Mair B, Wöhrle S, Wurm M, Mischerikow N, Roy MJ, Bader G, Greb P, Garavel G, Diers E, McLennan R, Whitworth C, Vetma V, Rumpel K, Scharnweber M, Fuchs JE, Gerstberger T, Cui Y, Gremel G, Chetta P, Hopf S, Budano N, Rinnenthal J, Gmaschitz G, Mayer M, Koegl M, Ciulli A, Weinstabl H, Farnaby W
OpenAccess logo Nat Commun 13 5969 (2022)
PMID: 36216795

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-154076 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Elongin-B Chain: A
Molecule details ›
Chain: A
Length: 104 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15370 (Residues: 1-104; Coverage: 88%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family
Elongin-C Chain: B
Molecule details ›
Chain: B
Length: 97 amino acids
Theoretical weight: 10.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15369 (Residues: 17-112; Coverage: 86%)
Gene names: ELOC, TCEB1
Sequence domains: Skp1 family, tetramerisation domain
von Hippel-Lindau disease tumor suppressor Chain: C
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 Chain: D

Ligands and Environments

2 bound ligands:
Ligand IOD 7 x IOD
Ligand IFJ 1 x IFJ
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 47.469Å b: 101.395Å c: 69.131Å
α: 90° β: 105.56° γ: 90°
R-values:
R R work R free
0.179 0.178 0.202
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader Probes.
Hartung et al. (2023)
8 more

3 mentions without citation

Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders.
Diehl et al. (2022)
2 more