8EA8

NKG2D complexed with inhibitor 4a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Identification of small-molecule protein-protein interaction inhibitors for NKG2D.

Thompson, A.A.Harbut, M.B.Kung, P.P.Karpowich, N.K.Branson, J.D.Grant, J.C.Hagan, D.Pascual, H.A.Bai, G.Zavareh, R.B.Coate, H.R.Collins, B.C.Cote, M.Gelin, C.F.Damm-Ganamet, K.L.Gholami, H.Huff, A.R.Limon, L.Lumb, K.J.Mak, P.A.Nakafuku, K.M.Price, E.V.Shih, A.Y.Tootoonchi, M.Vellore, N.A.Wang, J.Wei, N.Ziff, J.Berger, S.B.Edwards, J.P.Gardet, A.Sun, S.Towne, J.E.Venable, J.D.Shi, Z.Venkatesan, H.Rives, M.L.Sharma, S.Shireman, B.T.Allen, S.J.

(2023) Proc Natl Acad Sci U S A 120: e2216342120-e2216342120

  • DOI: https://doi.org/10.1073/pnas.2216342120
  • Primary Citation of Related Structures:  
    8EA5, 8EA6, 8EA7, 8EA8, 8EA9, 8EAA, 8EAB

  • PubMed Abstract: 

    NKG2D (natural-killer group 2, member D) is a homodimeric transmembrane receptor that plays an important role in NK, γδ + , and CD8 + T cell-mediated immune responses to environmental stressors such as viral or bacterial infections and oxidative stress. However, aberrant NKG2D signaling has also been associated with chronic inflammatory and autoimmune diseases, and as such NKG2D is thought to be an attractive target for immune intervention. Here, we describe a comprehensive small-molecule hit identification strategy and two distinct series of protein-protein interaction inhibitors of NKG2D. Although the hits are chemically distinct, they share a unique allosteric mechanism of disrupting ligand binding by accessing a cryptic pocket and causing the two monomers of the NKG2D dimer to open apart and twist relative to one another. Leveraging a suite of biochemical and cell-based assays coupled with structure-based drug design, we established tractable structure-activity relationships with one of the chemical series and successfully improved both the potency and physicochemical properties. Together, we demonstrate that it is possible, albeit challenging, to disrupt the interaction between NKG2D and multiple protein ligands with a single molecule through allosteric modulation of the NKG2D receptor dimer/ligand interface.


  • Organizational Affiliation

    Therapeutics Discovery, Janssen Research & Development, San Diego, CA 92121.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NKG2-D type II integral membrane proteinA [auth B],
B [auth A]
129Homo sapiensMutation(s): 2 
Gene Names: KLRK1D12S2489ENKG2D
UniProt & NIH Common Fund Data Resources
Find proteins for P26718 (Homo sapiens)
Explore P26718 
Go to UniProtKB:  P26718
PHAROS:  P26718
GTEx:  ENSG00000213809 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26718
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VML (Subject of Investigation/LOI)
Query on VML

Download Ideal Coordinates CCD File 
F [auth B]N-{(1S)-2-(dimethylamino)-2-oxo-1-[3-(trifluoromethyl)phenyl]ethyl}-4-[4-(trifluoromethyl)phenyl]pyridine-3-carboxamide
C24 H19 F6 N3 O2
ZMELGOOSPVFBKG-FQEVSTJZSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
G [auth B]
H [auth A]
I [auth A]
C [auth B],
D [auth B],
G [auth B],
H [auth A],
I [auth A],
K [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth B],
J [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.09α = 90
b = 43.675β = 125.01
c = 72.591γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary