SMTL ID : 9hg4.1

NACHT domain of NLRP3 in complex with DFV890

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

monomer

Ligands

1 x 01: 1-[azanyl-oxidanylidene-[2-(2-oxidanylpropan-2-yl)-1,3-thiazol-5-yl]-$l^{6}-sulfanylidene]-3-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)urea

01.1: 16 residues within 4Å: Chain A: A.98, A.99, R.222, P.223, M.279, I.282, V.285, T.310, Y.314, T.395, I.445, F.446, R.449, E.500, Y.503, M.532 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.282, A:V.285, A:T.310, A:Y.314, A:T.395, A:F.446, A:F.446, A:Y.503, A:Y.503 Hydrogen bonds: A:A.99, A:A.99, A:R.222, A:R.222, A:R.449, A:R.449, A:E.500 Water bridges: A:S.497

1 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.2: 17 residues within 4Å: Chain A: R.38, Y.39, T.40, L.42, A.98, G.100, I.101, G.102, K.103, T.104, I.105, F.244, Y.252, P.283, L.284, W.287, H.393 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.40, A:T.40, A:G.100, A:I.101, A:G.102, A:K.103, A:T.104, A:T.104, A:T.104, A:I.105 Water bridges: A:R.38, A:K.103, A:K.103, A:T.104, A:D.173, A:W.287 Salt bridges: A:K.103, A:H.393 pi-Stacking: A:F.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, D.M. et al., Discovery of DFV890, a Potent Sulfonimidamide-Containing NLRP3 Inflammasome Inhibitor. J.Med.Chem. (2025)

Release Date

2025-03-19

Peptides

NACHT, LRR and PYD domains-containing protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NACHT, LRR and PYD domains-containing protein 3

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