9GY3: CRBNmidi

Crystal structure of CRBNmidi in complex with (S)-dHTC1. Determined by X-ray diffraction at 2.5 Å resolution. Released 1 Oct 2025.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,240
Mol. weight: 76.44 kDa
Ligands: ZN, A1IQT
Released: 1 Oct 2025

Explore 9GY3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GY3 contains 20 α-helices and 44 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	48	1	1
α-helix	54-56	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	119-123	5	2
β-strand	127	1	3
β-strand	132	1	3
β-strand	135-147	13	2
β-strand	154-172	19	2
β-strand	178-184	7	2
α-helix	185-186	2
β-strand	188	1	4
α-helix	251-264	14
α-helix	277-287	11
α-helix	292-300	9
β-strand	303	1	4
α-helix	304-315	12
β-strand	320-323	4	5
β-strand	330-333	4	5
β-strand	337	1	6
β-strand	346-350	5	6
β-strand	356-362	7	6
β-strand	368-375	8	6
β-strand	384-391	8	6
β-strand	397-404	8	6
β-strand	410	1	1
β-strand	413-418	6	6
α-helix	419-421	3
β-strand	422-424	3	5

Chain C: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
α-helix	58-60	3
β-strand	65-66	2	7
α-helix	73-74	2
β-strand	78-83	6	7
β-strand	96-101	6	7
α-helix	104-113	10
β-strand	119-127	9	7
β-strand	132-147	16	7
β-strand	154-172	19	7
α-helix	177	1
β-strand	178-184	7	7
α-helix	185-186	2
β-strand	188	1	8
α-helix	251-264	14
α-helix	277-287	11
α-helix	292-300	9
β-strand	303	1	8
α-helix	304-314	11
β-strand	320-323	4	9
β-strand	330-333	4	9
β-strand	337	1	10
β-strand	341	1	11
β-strand	344	1	11
β-strand	346-350	5	10
β-strand	356-362	7	10
β-strand	368-375	8	10
β-strand	384-391	8	10
β-strand	397-404	8	10
β-strand	413-418	6	10
α-helix	419-421	3
β-strand	422-424	3	9

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

>9GY3_1 Protein cereblon (chains A, C)
SAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSIQVIPVLPQVMMILVPGQTLPL
QLFHPQEVSMVRNLIQNDRTFAVLAYSNVQEREAEFGTTAEIYAYREEQDFGIEIVKVKA
IGRQRFKVLELRTQSDGIQQAKVQILPEGSGDAETLMDRIKKQLREWDENLKDDSLPSNP
IDFSYWVAANLPIDDSLRIQLLKIDSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEI
FSLSREGPMAAYVNPHGYVHEILTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASH
IGWKFTATKKDMSPQKFWGLTRSALIPTI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
A1IQT	2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfo…	C33 H40 N8 O6 S	2

Primary citation

High-throughput diversification of protein-ligand surfaces to discover chemical inducers of proximity. Shaum, J.B., Munoz I Ordono, M., Steen, E.A. et al. bioRxiv (2025). DOI 10.1101/2024.09.30.615685 · 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
8RQ8 2.19 Å, Crystal structure of CRBN-midi in complex with mezigdomide
9OHR 2.34 Å, Structure of CRBN:IKZF2:Compound 35

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