9CUO

Crystal structure of CRBN with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01305
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon
A, B, C, D, E
A, B, C, D, E, F
113Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A0J (Subject of Investigation/LOI)
Query on A1A0J

Download Ideal Coordinates CCD File 
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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.47α = 90
b = 141.5β = 90
c = 141.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
REFMACphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release