SMTL ID : 6x86.1 (1 other biounit)

Crystal Structure of TNFalpha with indolinone compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

homo-trimer

Ligands

1 x UTY: 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile(Non-covalent)

UTY.1: 24 residues within 4Å: Chain A: K.12, L.58, Y.120, V.124, I.156, A.157, L.158 Chain B: L.58, Y.60, S.61, Y.120, L.121, G.122, G.123, Y.152, I.156 Chain C: K.12, L.58, I.59, Y.60, Y.120, G.122, G.123, L.158 15 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: A:L.58, A:L.58, A:V.124, A:L.158, C:L.58, C:L.158, B:L.58, B:Y.60, B:Y.120, B:Y.120, B:Y.152 Hydrogen bonds: C:K.12, C:Y.120, C:L.158, B:Y.152

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
A

B
B

C
C

Tumor necrosis factor

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