SMTL ID : 8se5.1

NKG2D complexed with inhibitor 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

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

PGE.1: 7 residues within 4Å: Chain A: K.53, K.60, N.90, L.91, T.93, S.108, F.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.53, A:T.93 PGE.2: 6 residues within 4Å: Chain A: Y.65, I.95, A.106, S.107, K.110, Y.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.107, A:K.110, A:Y.112 Water bridges: A:S.107 PGE.4: 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 PGE.5: 7 residues within 4Å: Chain B: K.53, N.90, L.91, L.92, T.93, S.108, F.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.53, B:T.93

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

PEG.3: 9 residues within 4Å: Chain A: N.15, I.17, Y.24, 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

1 x ZW7: 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(Non-covalent)

ZW7.6: 15 residues within 4Å: Chain A: I.17, F.26, 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 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.17, B:F.26, B:F.26, B:L.61, B:I.123, A:F.26, A:V.62, A:K.63 Hydrogen bonds: B:K.63, A:L.61, A:K.63 Water bridges: B:K.63, B:K.63, B:K.63 pi-Stacking: B:F.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Development of small molecule inhibitors of natural killer group 2D receptor (NKG2D). Bioorg.Med.Chem.Lett. (2023)

Release Date

2023-10-11

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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