9GAO: CRBNmidi

Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-methylacetamide. Determined by X-ray diffraction at 1.95 Å resolution. Released 2 Oct 2024.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,084
Mol. weight: 75.64 kDa
Ligands: ZN, A1IJM
Released: 2 Oct 2024

Explore 9GAO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GAO contains 23 α-helices and 36 β-strands across 2 chains. 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	48	1	1
α-helix	54-56	3
α-helix	58-60	3
β-strand	65-66	2	2
α-helix	73-74	2
β-strand	78-83	6	2
β-strand	96-101	6	2
α-helix	104-114	11
β-strand	119-127	9	2
α-helix	128-130	3
β-strand	132-149	18	2
β-strand	152-172	21	2
β-strand	178-184	7	2
α-helix	185-186	2
α-helix	251-264	14
α-helix	277-287	11
α-helix	292-300	9
α-helix	304-317	14
β-strand	320-323	4	3
β-strand	330-333	4	3
α-helix	334-336	3
β-strand	337	1	4
β-strand	346-350	5	4
β-strand	356-362	7	4
β-strand	368-375	8	4
β-strand	384-391	8	4
β-strand	397-404	8	4
β-strand	410	1	1
β-strand	413-418	6	4
α-helix	419-421	3
β-strand	422-424	3	3

Chain C: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
α-helix	58-60	3
β-strand	65-66	2	5
α-helix	73-74	2
β-strand	78-83	6	5
β-strand	96-101	6	5
α-helix	104-114	11
β-strand	119-127	9	5
α-helix	128-130	3
β-strand	132-149	18	5
β-strand	152-172	21	5
β-strand	178-184	7	5
α-helix	185-186	2
α-helix	251-264	14
α-helix	277-287	11
α-helix	292-300	9
α-helix	304-317	14
β-strand	320-323	4	6
β-strand	330-333	4	6
α-helix	334-336	3
β-strand	337	1	7
β-strand	346-350	5	7
β-strand	356-362	7	7
β-strand	368-375	8	7
β-strand	384-391	8	7
β-strand	397-404	8	7
β-strand	413-418	6	7
β-strand	422-424	3	6

Molecules and chains

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

Sequence of entity 1 (A, C), FASTA

>9GAO_1 Protein cereblon (chains A, C)
SAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSIQVIPVLPQVMMILVPGQTLPL
QLFHPQEVSMVRNLIQNDRTFAVLAYSNVQEREAEFGTTAEIYAYREEQDFGIEIVKVKA
IGRQRFKVLELRTQSDGIQQAKVQILPEGSGDAETLMDRIKKQLREWDENLKDDSLPSNP
IDFSYWVAANLPIDDSLRIQLLKIDSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEI
FSLSREGPMAAYVNPHGYVHEILTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASH
IGWKFTATKKDMSPQKFWGLTRSALIPTI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
A1IJM	2-[4-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]phenoxy]-~{N}-methyl-ethanam…	C14 H16 N2 O4	2

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
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
8RQ8 2.19 Å, Crystal structure of CRBN-midi in complex with mezigdomide
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

Browse structure collections

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