SMTL ID : 8eab.1

NKG2D complexed with inhibitor 4f

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: N.15, Q.25, F.26 Chain B: Y.19, D.57, L.58, L.61 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.19 Hydrogen bonds: A:F.26 PEG.3: 8 residues within 4Å: Chain A: Y.19, D.57, L.58, L.61 Chain B: I.17, Y.24, Q.25, F.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.26, B:F.26

1 x VN2: N-[(1S)-2-oxo-1-[3-(trifluoromethyl)phenyl]-2-({4-[4-(trifluoromethyl)phenyl]pyridin-3-yl}amino)ethyl]-4-[4-(trifluoromethyl)phenyl]pyridine-3-carboxamide(Non-covalent)

VN2.2: 19 residues within 4Å: Chain A: I.17, Y.24, Q.25, F.26, L.58, L.61, V.62, K.63, H.66, I.123 Chain B: I.17, Y.24, Q.25, F.26, L.61, V.62, K.63, H.66, I.123 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:I.17, A:F.26, A:F.26, A:L.61, A:I.123, B:F.26, B:F.26, B:F.26, B:F.26, B:L.61, B:V.62, B:I.123 Hydrogen bonds: A:L.61, A:K.63, B:L.61, B:K.63, B:K.63 pi-Stacking: A:F.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.A. et al., Identification of small-molecule protein-protein interaction inhibitors for NKG2D. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-05-03

Peptides

NKG2-D type II integral membrane protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NKG2-D type II integral membrane protein

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