SMTL ID : 8se6.1

NKG2D complexed with inhibitor 36

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-dimer

Ligands

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

PGE.1: 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.2: 5 residues within 4Å: Chain A: Y.65, M.97, L.104, Y.112, E.114 No protein-ligand interaction detected (PLIP) PGE.3: 6 residues within 4Å: Chain A: K.53, 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.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 ZWA: N-[(1S)-2-(dimethylamino)-2-oxo-1-{3-[3-(2,2,2-trifluoroethyl)azetidin-1-yl]phenyl}ethyl]-4'-(trifluoromethyl)[1,1'-biphenyl]-2-carboxamide(Non-covalent)

ZWA.4: 18 residues within 4Å: Chain A: I.17, F.26, L.61, V.62, K.63, H.66 Chain B: I.17, Y.19, Y.24, Q.25, F.26, L.58, L.59, L.61, V.62, K.63, H.66, I.123 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.26, A:V.62, A:K.63, B:F.26, B:F.26, B:L.58, B:V.62, B:I.123 Hydrogen bonds: A:L.61, A:K.63, B:K.63 pi-Stacking: B:F.26

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 7 residues within 4Å: Chain B: N.44, S.46, K.49, Y.51, M.125, Q.126, R.127 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.44, B:R.127 Water bridges: B:K.49

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
A

B
B

NKG2-D type II integral membrane protein

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