9CUO | pdb_00009cuo

Crystal structure of CRBN with compound 3

PDB DOI: https://doi.org/10.2210/pdb9CUO/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-26 Released: 2024-08-28
Deposition Author(s): Zheng, X., Ji, N., Campbell, V., Slavin, A., Zhu, X., Chen, D., Rong, H., Enerson, B., Mayo, M., Sharma, K., Browne, C.M., Klaus, C.R., Li, H., Massa, G., McDonald, A.A., Shi, Y., Sintchak, M., Skouras, S., Walther, D.M., Yuan, K., Zhang, Y., Kelleher, J., Guang, L., Luo, X., Mainolfi, N., Weiss, M.M.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.205 (Depositor), 0.208 (DCC)
R-Value Work:
0.155 (Depositor), 0.162 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of KT-474─a Potent, Selective, and Orally Bioavailable IRAK4 Degrader for the Treatment of Autoimmune Diseases.

Zheng, X., Ji, N., Campbell, V., Slavin, A., Zhu, X., Chen, D., Rong, H., Enerson, B., Mayo, M., Sharma, K., Browne, C.M., Klaus, C.R., Li, H., Massa, G., McDonald, A.A., Shi, Y., Sintchak, M., Skouras, S., Walther, D.M., Yuan, K., Zhang, Y., Kelleher, J., Liu, G., Luo, X., Mainolfi, N., Weiss, M.M.

(2024) J Med Chem 67: 18022-18037

PubMed: 39151120 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c01305
Primary Citation Related Structures:
9CUO

PubMed Abstract:
Interleukin-1 receptor associated kinase 4 (IRAK4) is an essential mediator of the IL-1R and TLR signaling pathways, both of which have been implicated in multiple autoimmune conditions. Hence, blocking the activity of IRAK4 represents an attractive approach for the treatment of autoimmune diseases. The activity of this serine/threonine kinase is dependent on its kinase and scaffolding activities; thus, degradation represents a potentially superior approach to inhibition. Herein, we detail the exploration of structure-activity relationships that ultimately led to the identification of KT-474, a potent, selective, and orally bioavailable heterobifunctional IRAK4 degrader. This represents the first heterobifunctional degrader evaluated in a nononcology indication and dosed to healthy human volunteers. This molecule successfully completed phase I studies in healthy adult volunteers and patients with atopic dermatitis or hidradenitis suppurativa. Phase II clinical trials in both of these indications have been initiated.

Organizational Affiliation

Kymera Therapeutics, 500 N. Beacon Street, Fourth Floor, Watertown, Massachusetts 02472, United States.

Macromolecule Content

Total Structure Weight: 79.19 kDa
Atom Count: 5,207
Modeled Residue Count: 568
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A, B, C, D, E A, B, C, D, E, F	113	Homo sapiens	Mutation(s): 0 Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens) Explore Q96SW2 Go to UniProtKB: Q96SW2
PHAROS: Q96SW2 GTEx: ENSG00000113851
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96SW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A0J (Subject of Investigation/LOI) Query on A1A0J Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain NA [auth F] SDF format, chain X [auth D] SDF format, chain S [auth C] SDF format, chain M [auth B] SDF format, chain EA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain X [auth D] MOL2 format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain EA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain X [auth D] mmCIF format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain EA [auth E]	EA [auth E] H [auth A] M [auth B] NA [auth F] S [auth C] EA [auth E], H [auth A], M [auth B], NA [auth F], S [auth C], X [auth D]	(3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione C₁₃ H₁₃ N₃ O₃ VFDZUWPTOYTMAL-JTQLQIEISA-N		Interactions Focus chain EA [auth E] Focus chain H [auth A] Focus chain M [auth B] Focus chain NA [auth F] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain EA [auth E] Focus chain H [auth A] Focus chain M [auth B] Focus chain NA [auth F] Focus chain S [auth C] Focus chain X [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain V [auth C] SDF format, chain PA [auth F] SDF format, chain OA [auth F] SDF format, chain FA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain V [auth C] MOL2 format, chain PA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain FA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain V [auth C] mmCIF format, chain PA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain FA [auth E]	FA [auth E] I [auth A] J [auth A] N [auth B] O [auth B] FA [auth E], I [auth A], J [auth A], N [auth B], O [auth B], OA [auth F], P [auth B], PA [auth F], T [auth C], U [auth C], V [auth C], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain MA [auth F] SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain MA [auth F] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	DA [auth E] G [auth A] L [auth B] MA [auth F] R [auth C] DA [auth E], G [auth A], L [auth B], MA [auth F], R [auth C], W [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain G [auth A] Focus chain L [auth B] Focus chain MA [auth F] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain DA [auth E] Focus chain G [auth A] Focus chain L [auth B] Focus chain MA [auth F] Focus chain R [auth C] Focus chain W [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain HA [auth E] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain LA [auth E] SDF format, chain K [auth A] SDF format, chain IA [auth E] SDF format, chain GA [auth E] SDF format, chain CA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain LA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain LA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] GA [auth E] HA [auth E] AA [auth D], BA [auth D], CA [auth D], GA [auth E], HA [auth E], IA [auth E], JA [auth E], K [auth A], KA [auth E], LA [auth E], Q [auth B], QA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain Q [auth B] Focus chain QA [auth F] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain Q [auth B] Focus chain QA [auth F]