8RQ8: CRBN-midi

Crystal structure of CRBN-midi in complex with mezigdomide. Determined by X-ray diffraction at 2.19 Å resolution. Released 25 Sept 2024.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,480
Mol. weight: 38.11 kDa
Ligands: ZN, QFC
Released: 25 Sept 2024

Explore 8RQ8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RQ8 contains 11 α-helices and 17 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
α-helix	58-60	3
β-strand	65-66	2	1
α-helix	73-74	2
β-strand	78-83	6	1
α-helix	84	1
β-strand	96-101	6	1
α-helix	104-115	12
β-strand	119-124	6	1
β-strand	135-149	15	1
β-strand	152-172	21	1
β-strand	178-184	7	1
α-helix	185-186	2
α-helix	251-264	14
α-helix	277-287	11
α-helix	292-300	9
α-helix	304-316	13
β-strand	321-323	3	2
β-strand	330-332	3	2
α-helix	334-336	3
β-strand	337	1	3
β-strand	346-350	5	3
β-strand	356-362	7	3
β-strand	368-375	8	3
β-strand	384-391	8	3
β-strand	397-404	8	3
β-strand	413-418	6	3
β-strand	422-424	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	A	protein	329	Homo sapiens	Q96SW2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8RQ8_1 Protein cereblon (chains A)
SAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSIQVIPVLPQVMMILVPGQTLPL
QLFHPQEVSMVRNLIQNDRTFAVLAYSNVQEREAEFGTTAEIYAYREEQDFGIEIVKVKA
IGRQRFKVLELRTQSDGIQQAKVQILPEGSGDAETLMDRIKKQLREWDENLKDDSLPSNP
IDFSYWVAANLPIDDSLRIQLLKIDSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEI
FSLSREGPMAAYVNPHGYVHEILTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASH
IGWKFTATKKDMSPQKFWGLTRSALIPTI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
QFC	Mezigdomide	C32 H30 F N5 O4	1

Primary citation

Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders. Kroupova, A., Spiteri, V.A., Rutter, Z.J. et al. Nat Commun (2024) 15:8885-8885. DOI 10.1038/s41467-024-52871-9 · PubMed

Other PDB entries of the same protein (UniProt Q96SW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4M91 1.1 Å, crystal structure of hN33/Tusc3-peptide 1
9CUO 1.6 Å, Crystal structure of CRBN with compound 3
9OHQ 1.6 Å, Structure of CRBN:IKZF2:Compound 15
9DOM 1.69 Å, PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of…
7BQV 1.8 Å, Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide
9O91 1.86 Å, Structure of IKZF2:CRBN:Compound 5 ternary structure
7BQU 1.9 Å, Cereblon in complex with SALL4 and (S)-thalidomide
9GAO 1.95 Å, Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-me…
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
8RQC 2.15 Å, Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2
9OHR 2.34 Å, Structure of CRBN:IKZF2:Compound 35
9SFM 2.39 Å, Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide

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