SMTL ID : 6ooy.1

Asymmetric hTNF-alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 7 residues within 4Å: Chain A: Y.59, S.60, L.120 Chain B: Y.119 Chain C: Y.119, Y.151 Ligands: A7M.2 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.121, C:Y.151 Hydrophobic interactions: C:Y.119, C:Y.119

1 x A7M: {1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}methanol(Non-covalent)

A7M.2: 14 residues within 4Å: Chain A: L.57, Y.59, V.123, L.157 Chain B: Y.119, G.121, G.122 Chain C: L.57, Y.59, S.60, Y.119, L.120, Y.151 Ligands: MRD.1 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:L.57, A:L.57, A:L.57, A:Y.59, A:V.123, A:L.157, C:L.57, C:Y.59, C:Y.151 Hydrogen bonds: C:L.120, C:Y.151 pi-Stacking: C:Y.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O'Connell, J. et al., Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer. Nat Commun (2019)

Release Date

2019-12-25

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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