8SE5

NKG2D complexed with inhibitor 14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development of small molecule inhibitors of natural killer group 2D receptor (NKG2D).

Wang, J.Nakafuku, K.M.Ziff, J.Gelin, C.F.Gholami, H.Thompson, A.A.Karpowich, N.K.Limon, L.Coate, H.R.Damm-Ganamet, K.L.Shih, A.Y.Grant, J.C.Cote, M.Mak, P.A.Pascual, H.A.Rives, M.L.Edwards, J.P.Venable, J.D.Venkatesan, H.Shi, Z.Allen, S.J.Sharma, S.Kung, P.P.Shireman, B.T.

(2023) Bioorg Med Chem Lett 96: 129492-129492

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129492
  • Primary Citation of Related Structures:  
    8SE5, 8SE6

  • PubMed Abstract: 

    Natural killer group 2D (NKG2D) is a homodimeric activating immunoreceptor whose function is to detect and eliminate compromised cells upon binding to the NKG2D ligands (NKG2DL) major histocompatibility complex (MHC) molecules class I-related chain A (MICA) and B (MICB) and UL16 binding proteins (ULBP1-6). While typically present at low levels in healthy cells and tissue, NKG2DL expression can be induced by viral infection, cellular stress or transformation. Aberrant activity along the NKG2D/NKG2DL axis has been associated with autoimmune diseases due to the increased expression of NKG2D ligands in human disease tissue, making NKG2D inhibitors an attractive target for immunomodulation. Herein we describe the discovery and optimization of small molecule PPI (protein-protein interaction) inhibitors of NKG2D/NKG2DL. Rapid SAR was guided by structure-based drug design and accomplished by iterative singleton and parallel medicinal chemistry synthesis. These efforts resulted in the identification of several potent analogs (14, 21, 30, 45) with functional activity and improved LLE.


  • Organizational Affiliation

    Janssen Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA, 92121, United States. Electronic address: jwang301@its.jnj.com.


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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZW7 (Subject of Investigation/LOI)
Query on ZW7

Download Ideal Coordinates CCD File 
H [auth A]N-{(1S)-2-[(1R,5S,6S)-6-(hydroxymethyl)-3-azabicyclo[3.1.0]hexan-3-yl]-2-oxo-1-[3-(trifluoromethyl)phenyl]ethyl}-4'-(trifluoromethyl)[1,1'-biphenyl]-2-carboxamide
C29 H24 F6 N2 O3
LLNURPOWMDHYAG-LIONHTAISA-N
PGE
Query on PGE

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.21α = 90
b = 43.361β = 102.87
c = 64.526γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata scaling
xia2data reduction
PHASERphasing

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: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary