SMTL ID : 6x83.2 (1 other biounit)

Crystal Structure of TNFalpha with fragment compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-trimer

Ligands

2 x UTS: 1-benzyl-1H-benzimidazole(Non-covalent)

UTS.1: 15 residues within 4Å: Chain A: L.58, I.59, Y.60, G.122, G.123 Chain B: L.58, Y.60, S.61, Y.120, L.121, G.122, G.123, Y.152 Chain C: Y.60 Ligands: UTS.2 8 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:L.58, B:Y.60, A:L.58, A:Y.60, C:Y.60 Hydrogen bonds: B:Y.152 pi-Stacking: B:Y.120, B:Y.120 UTS.2: 13 residues within 4Å: Chain A: L.58, Y.60, S.61, Y.120, L.121, Y.152 Chain B: Y.120 Chain C: L.58, Y.60, Y.120, L.121, G.122 Ligands: UTS.1 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:Y.60, A:Y.120, A:Y.120, C:L.58, C:Y.120 pi-Stacking: A:Y.60, B:Y.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dietrich, J.D. et al., Development of Orally Efficacious Allosteric Inhibitors of TNF alpha via Fragment-Based Drug Design. J.Med.Chem. (2021)

Release Date

2021-01-13

Peptides

Tumor necrosis factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Tumor necrosis factor

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