9Q8V | pdb_00009q8v

Cryo-EM structure of the NLRP3 decamer bound to the inhibitor BAL-1516

PDB DOI: https://doi.org/10.2210/pdb9Q8V/pdb
EM Map EMD-52908: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-02-25 Released: 2026-09-09
Deposition Author(s): Torp, J., Wilhelmsen, K., Hartman, G., Hagelueken, G., Geyer, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9Q8V

This is version 1.0 of the entry. See complete history.

Literature

Inhibition of NLRP3 by a CNS-penetrating indazole scaffold

Torp, J., Geyer, M.

To be published.

Macromolecule Content

Total Structure Weight: 1,192.11 kDa
Atom Count: 67,130
Modeled Residue Count: 8,330
Deposited Residue Count: 10,360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NACHT, LRR and PYD domains-containing protein 3	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	1,036	Homo sapiens	Mutation(s): 0 Gene Names: NLRP3, C1orf7, CIAS1, NALP3, PYPAF1 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P20 (Homo sapiens) Explore Q96P20 Go to UniProtKB: Q96P20
PHAROS: Q96P20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96P20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I4G Query on A1I4G Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain KA [auth I] SDF format, chain M [auth A] SDF format, chain NA [auth J] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	BA [auth F] EA [auth G] HA [auth H] KA [auth I] M [auth A] BA [auth F], EA [auth G], HA [auth H], KA [auth I], M [auth A], NA [auth J], P [auth B], S [auth C], V [auth D], Y [auth E]	3-ethoxy-~{N}-methyl-~{N}-[(1~{R})-1-(4-methyl-1~{H}-pyrazolo[4,3-c]pyridin-7-yl)ethyl]-4-(4-methyl-1,3-thiazol-2-yl)benzamide C₂₃ H₂₅ N₅ O₂ S MFSJYCVXQNOKQW-OAHLLOKOSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain IA [auth I] SDF format, chain K [auth A] SDF format, chain LA [auth J] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth J] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain IA [auth I] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth J] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	CA [auth G] FA [auth H] IA [auth I] K [auth A] LA [auth J] CA [auth G], FA [auth H], IA [auth I], K [auth A], LA [auth J], N [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain IA [auth I] Focus chain K [auth A] Focus chain LA [auth J] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain IA [auth I] Focus chain K [auth A] Focus chain LA [auth J] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain GA [auth H] SDF format, chain JA [auth I] SDF format, chain L [auth A] SDF format, chain MA [auth J] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain JA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain JA [auth I] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	AA [auth F] DA [auth G] GA [auth H] JA [auth I] L [auth A] AA [auth F], DA [auth G], GA [auth H], JA [auth I], L [auth A], MA [auth J], O [auth B], R [auth C], U [auth D], X [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain JA [auth I] Focus chain L [auth A] Focus chain MA [auth J] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain JA [auth I] Focus chain L [auth A] Focus chain MA [auth J] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	GE 976/16-1
German Research Foundation (DFG)	Germany	EXC2151-390873048

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.