SMTL ID : 9ojy.1 (1 other biounit)

Crystal structure of TNF alpha in complex with compound 3.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-trimer

Ligands

1 x 01: (6R,13R,14S)-1-(difluoromethoxy)-11-[2-(2-hydroxypropan-2-yl)pyrimidin-5-yl]-7H-6,14-methanopyrido[3',2':4,5]imidazo[1,2-b][2,5]benzodiazocin-5(14H)-one

01.1: 19 residues within 4Å: Chain A: L.58, Y.120, V.124, I.156, L.158 Chain B: L.58, Y.60, S.61, Y.120, L.121, Y.152, I.156, L.158 Chain C: L.58, I.59, Y.60, Y.120, G.122, L.158 14 PLIP interactions: 4 interactions with chain C, 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:L.58, C:Y.120, C:L.158, A:L.58, A:L.58, A:L.58, A:V.124, A:I.156, A:L.158, B:L.58, B:L.158 Halogen bonds: C:I.59 Hydrogen bonds: A:Y.120 pi-Stacking: B:Y.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bian, Z. et al., Discovery of Orally Efficacious Bridged Piperazines as smTNF Modulators. J.Med.Chem. (2025)

Release Date

2025-07-23

Peptides

Tumor necrosis factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Tumor necrosis factor

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