SMTL ID : 8zem.1

Crystal Structure of NLRP3 NACHT domain in complex with NP3-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.32 Å

Oligo State

monomer

Ligands

1 x 01: 1-[5-[2,3-bis(chloranyl)phenyl]-2,3-dihydro-1~{H}-inden-4-yl]-3-[4-(2-oxidanylpropan-2-yl)thiophen-2-yl]sulfonyl-urea

01.1: 18 residues within 4Å: Chain A: A.99, A.100, R.223, P.224, V.225, F.282, I.283, V.286, T.311, Y.315, I.446, F.447, R.450, Q.496, S.498, E.501, Y.504, D.534 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.225, A:I.283, A:V.286, A:F.447, A:F.447, A:Y.504 Hydrogen bonds: A:A.100, A:A.100, A:R.223, A:R.450, A:R.450, A:E.501

1 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.2: 18 residues within 4Å: Chain A: R.39, Y.40, T.41, L.43, A.99, A.100, G.101, I.102, G.103, K.104, T.105, I.106, Y.253, P.284, L.285, W.288, H.394, M.395 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.41, A:T.41, A:G.101, A:I.102, A:G.103, A:K.104, A:T.105, A:T.105, A:T.105, A:I.106 Salt bridges: A:K.104, A:H.394, A:H.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, C. et al., Deep-Learning-Driven Discovery of SN3-1, a Potent NLRP3 Inhibitor with Therapeutic Potential for Inflammatory Diseases. J.Med.Chem. (2024)

Release Date

2024-10-02

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