9ODR: CRBN TBD

Structure of CRBN TBD bound to compound C1. Determined by X-ray diffraction at 2.42 Å resolution. Released 28 May 2025.

Method: X-ray diffraction
Resolution: 2.42 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,537
Mol. weight: 50.92 kDa
Ligands: A1CAV, ZN
Released: 28 May 2025

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

Secondary structure: helices and β-sheets

9ODR contains 8 α-helices and 42 β-strands across 4 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.

Chains A and B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	320-323	4	1
β-strand	330-333	4	1
α-helix	334-336	3
β-strand	337	1	2
β-strand	343	1	3
β-strand	346-350	5	2
β-strand	356-362	7	2
β-strand	368-375	8	2
β-strand	384-391	8	2
β-strand	397-404	8	2
β-strand	413-418	6	2
α-helix	419-421	3
β-strand	422-423	2	1

Chains C and D: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	320-323	4	5
β-strand	330-333	4	5
α-helix	334-336	3
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	413-418	6	6
α-helix	419-421	3
β-strand	422-423	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	A, B, C, D	protein	111	Homo sapiens	Q96SW2 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9ODR_1 Protein cereblon (chains A, B, C, D)
GPSTSLSCKQCQETEITTKNEIFSLSLSGPMAAYVNPHGYVHETLTVYKASNLNLIGRPS
TEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTI

Ligands and cofactors

ID	Name	Formula	Copies
A1CAV	(3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl…	C19 H21 N3 O4	4
ZN	Zinc ion	Zn	4

Primary citation

Discovery and Characterization of PVTX-321 as a Potent and Orally Bioavailable Estrogen Receptor Degrader for ER+/HER2- Breast Cancer. Xu, G., Havens, C.G., Deng, Q. et al. J Med Chem (2025) 68:11299-11321. DOI 10.1021/acs.jmedchem.5c00223 · 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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