9CUO: CRBN with compound 3

Crystal structure of CRBN with compound 3. Determined by X-ray diffraction at 1.6 Å resolution. Released 28 Aug 2024.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,207
Mol. weight: 79.19 kDa
Ligands: A1A0J, ZN
Released: 28 Aug 2024

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

Secondary structure: helices and β-sheets

9CUO contains 12 α-helices and 54 β-strands across 6 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 C: 2 helices, 9 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	359-362	4	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	422-425	4	1

Chain B: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	320-323	4	3
β-strand	330-333	4	3
α-helix	334-336	3
β-strand	337	1	4
β-strand	359-362	4	4
β-strand	368-375	8	4
β-strand	384-391	8	4
β-strand	397-404	8	4
β-strand	413-418	6	4
α-helix	419-421	3
β-strand	422-423	2	3

Chains D and F: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	320-323	4	7
β-strand	330-333	4	7
α-helix	334-336	3
β-strand	337-338	2	8
β-strand	359-362	4	8
β-strand	368-375	8	8
β-strand	384-391	8	8
β-strand	397-404	8	8
β-strand	413-418	6	8
α-helix	419-421	3
β-strand	422-423	2	7

Chain E: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	320-323	4	9
β-strand	330-333	4	9
α-helix	334-336	3
β-strand	337-338	2	10
β-strand	359-362	4	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, B, C, D, E, F	protein	113	Homo sapiens	Q96SW2 (AlphaFold model)

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

>9CUO_1 Protein cereblon (chains A, B, C, D, E, F)
SGSPTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRP
STEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIP

Ligands and cofactors

ID	Name	Formula	Copies
A1A0J	(3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione	C13 H13 N3 O3	6
ZN	Zinc ion	Zn	6

Water and common crystallization additives (EDO, SO4) are not listed.

Primary citation

Discovery of KT-474─a Potent, Selective, and Orally Bioavailable IRAK4 Degrader for the Treatment of Autoimmune Diseases. Zheng, X., Ji, N., Campbell, V. et al. J Med Chem (2024) 67:18022-18037. DOI 10.1021/acs.jmedchem.4c01305 · 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
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
9SFM 2.39 Å, Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide

Browse structure collections

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