SMTL ID : 8ea5.1

NKG2D complexed with inhibitor 1a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

1 x VN8: (3S,5aS,8aR)-3-benzyl-6-[(3,5-dichlorophenyl)methyl]-1,4-dimethyloctahydropyrrolo[3,2-e][1,4]diazepine-2,5-dione(Non-covalent)

VN8.1: 14 residues within 4Å: Chain A: I.17, F.26, L.58, L.61, V.62, K.63 Chain B: I.17, Y.24, F.26, L.58, L.59, L.61, V.62, K.63 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.17, A:F.26, A:L.58, A:L.58, A:L.61, A:V.62, B:Y.24, B:F.26, B:L.58, B:L.59 Hydrogen bonds: A:K.63, B:K.63 pi-Stacking: A:F.26

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 7 residues within 4Å: Chain A: K.53, N.90, L.91, L.92, T.93, S.108, F.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.53 PGE.3: 6 residues within 4Å: Chain B: K.53, N.90, L.91, T.93, S.108, F.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.53, B:T.93

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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