SMTL ID : 8ri2.1

Crystal structure of NLRP3 in complex with inhibitor NP3-562

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x 01: 2-[4-chloranyl-9-oxidanylidene-12-(2-oxidanylpropan-2-yl)-5-thia-1,10,11-triazatricyclo[6.4.0.0^{2,6}]dodeca-2(6),3,7,11-tetraen-10-yl]-~{N}-[(3~{R})-1-methylpiperidin-3-yl]ethanamide

01.1: 16 residues within 4Å: Chain A: A.98, A.99, V.224, I.282, L.284, T.310, Y.314, T.395, F.446, R.449, Q.495, S.497, L.499, E.500, Y.503, M.532 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.98, A:I.282, A:I.282, A:T.310, A:F.446, A:L.499, A:E.500, A:Y.503, A:Y.503 Hydrogen bonds: A:R.449, A:R.449, A:D.533 Water bridges: A:Y.503 Salt bridges: A:E.500 Halogen bonds: A:Y.314

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 18 residues within 4Å: Chain A: R.38, Y.39, T.40, L.42, A.98, A.99, G.100, I.101, G.102, K.103, T.104, I.105, F.244, Y.252, P.283, L.284, W.287, H.393 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.40, A:T.40, A:A.98, 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: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

Velcicky, J. et al., Discovery of Potent, Orally Bioavailable, Tricyclic NLRP3 Inhibitors. J.Med.Chem. (2024)

Release Date

2024-01-17

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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