8Z0Z | pdb_00008z0z

Cryo-EM structure of the panda P2X7 receptor in complex with JNJ-54175446


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8Z0Z

This is version 1.3 of the entry. See complete history

Literature

Understanding interspecies drug response variations between human and rodent P2X7 receptors.

Guo, C.R.Sheng, D.Li, J.Y.Li, T.T.Yao, J.B.Zhang, R.Huang, Y.Zhao, Y.Y.Wang, D.P.Chen, J.Li, J.Wang, J.Zhou, Y.Shen, C.Jin, F.Cao, P.Hattori, M.Liu, H.Yu, Y.

(2025) Nat Commun 16: 10827-10827

  • DOI: https://doi.org/10.1038/s41467-025-65847-0
  • Primary Citation Related Structures: 
    8Z0Z, 8Z1D

  • PubMed Abstract: 

    Despite intensive development, P2X7 modulators have struggled in translation due to human genetic variability and species-dependent drug responses. Here, we identify PSFL1191, a portal-of-central-pocket (PCP)-site inhibitor selective for human and panda P2X7, but inactive against rodents. Cryo-EM structures revealed two distinct PCP sub-pockets: PCP1, a rigid base pocket demanding precise steric complementarity with PSFL1191, and PCP2, a conserved middle cavity targeted by JNJ-54175446, a clinical candidate unaffected by species differences. Species selectivity maps to a deep PCP1 motif (V312-Y295-M105-F103-P96). In P2rx7 A312V/A312V mice, PSFL1191 markedly altered macrophage-mediated bacterial clearance and wound healing while preserving basal physiology, effects absent in wild-type animals. Our findings establish the structural basis for interspecies pharmacological divergence in P2X7 modulation and highlight transgenic models as powerful tools for predicting therapeutic efficacy, thereby enabling more precise and efficient drug discovery.


  • Organizational Affiliation
    • School of Basic Medicine and Clinical Pharmacy and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.

Macromolecule Content 

  • Total Structure Weight: 118.8 kDa 
  • Atom Count: 7,470 
  • Modeled Residue Count: 960 
  • Deposited Residue Count: 1,026 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
P2X purinoceptor
A, B, C
342Ailuropoda melanoleucaMutation(s): 0 
Gene Names: PANDA_000894
UniProt
Find proteins for G1M6C4 (Ailuropoda melanoleuca)
Explore G1M6C4 
Go to UniProtKB:  G1M6C4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1M6C4
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L0I

Query on A1L0I



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
L [auth C]
JNJ-54175446
C18 H13 Cl F4 N6 O
CWFVVQFVGMFTBD-SECBINFHSA-N
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
G [auth B]
H [auth B]
J [auth C]
D [auth A],
E [auth A],
G [auth B],
H [auth B],
J [auth C],
K [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Data collection
  • Version 1.2: 2025-11-26
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2026-05-06
    Changes: Data collection, Database references