SMTL ID : 8eaa.1

NKG2D complexed with inhibitor 4e

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

1 x VMW: N-{(1S)-2-(dimethylamino)-1-[3-methyl-5-(trifluoromethyl)phenyl]-2-oxoethyl}-4-[4-(trifluoromethyl)phenyl]pyridine-3-carboxamide(Non-covalent)

VMW.1: 16 residues within 4Å: Chain A: I.17, F.26, L.58, L.61, V.62, K.63, H.66 Chain B: I.17, Y.24, Q.25, F.26, L.58, L.61, V.62, K.63, I.123 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.26, A:V.62, B:F.26, B:F.26, B:I.123 Hydrogen bonds: A:L.61, A:K.63, B:K.63 pi-Stacking: B:F.26

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

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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain B: Y.34, G.100, D.101, N.115, C.116, S.117 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.101, B:N.115, B:C.116, B:S.117, B:S.117 Water bridges: B:S.117

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
B

B
A

NKG2-D type II integral membrane protein

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