9UNY | pdb_00009uny

Natural product inhibitor of glyceraldehyde-3-phosphate dehydrogenase(GAPDH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.282 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

GAPDH inhibition by oridonin integrates glycolytic inhibition and anti-inflammation to alleviate rheumatoid arthritis synovitis.

Xiao, Q.Zhou, H.Li, M.Peng, Y.Huang, Y.Zhao, Y.Chen, S.Chen, H.Zhang, C.Yuan, Q.Qiu, L.He, Y.Dai, Z.Peng, T.Fu, Q.

(2026) Phytomedicine 160: 158650-158650

  • DOI: https://doi.org/10.1016/j.phymed.2026.158650
  • Primary Citation Related Structures: 
    9UNY

  • PubMed Abstract: 

    Current therapeutic strategies for rheumatoid arthritis (RA) synovitis rely primarily on immunosuppression, with limited options targeting the diseased synovial fibroblasts (FLSs). Modulating the metabolic state of FLSs has been proposed as a potential approach to shift them toward an anti-inflammatory phenotype and alleviate synovitis. However, the molecular mechanisms that bridge FLS metabolism to anti-inflammatory defense remain largely unexplored. We aimed to identify the target of ORI in synovial cells and to elucidate the molecular mechanism by which ORI alleviates RA synovitis. The therapeutic effects of oridonin were first assessed in an IL-1β-induced MH7A cell model of synovitis. Its direct protein target was identified using CC-ABPP, surface plasmon resonance (SPR), pull-down, cellular thermal shift assay (CETSA), and drug affinity responsive target stability (DARTS) assays. The specific binding site was confirmed by co-crystallization, LC-MS/MS analysis, and site-directed mutagenesis of GAPDH. The underlying mechanisms were investigated using Western blot, ELISA, immunofluorescence, RT-qPCR, HPLC, and metabolomics in FLSs. Furthermore, therapeutic efficacy and pathway validation were examined in GAPDH-knockdown mice with adjuvant-induced arthritis using immunohistochemistry and hematoxylin-eosin (HE) staining for pathological assessment. This study identified GAPDH as the direct target of oridonin in MH7A cells. ORI covalently binds to Cys152 of GAPDH, thereby inhibiting GAPDH enzymatic activity. Metabolomics data revealed an interruption in the glycolytic process. Metabolite analysis revealed the accumulation of methylglyoxal, which further activated the KEAP1-NRF2/HO-1 signaling pathway and suppressed the NF-κB signaling pathway. The existence of GAPDH-KEAP1-NRF2 and NF-κB signal pathways were validated in both cell with GAPDH siRNA and GAPDH +/- mice with adjuvant-induced arthritis for the first time. GAPDH inhibition by oridonin induces intracellular accumulation of methylglyoxal, which activates KEAP1-NRF2/HO-1 signaling pathway and suppresses NF-κB signaling pathway.


  • Organizational Affiliation
    • Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, China.

Macromolecule Content 

  • Total Structure Weight: 147.42 kDa 
  • Atom Count: 10,509 
  • Modeled Residue Count: 1,332 
  • Deposited Residue Count: 1,340 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenaseA [auth P],
B [auth A],
C [auth B],
D [auth C]
335Homo sapiensMutation(s): 0 
Gene Names: GAPDHGAPDCDABP0047OK/SW-cl.12
EC: 1.2.1.12 (PDB Primary Data), 2.6.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P04406 (Homo sapiens)
Explore P04406 
Go to UniProtKB:  P04406
PHAROS:  P04406
GTEx:  ENSG00000111640 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04406
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EP4

Query on A1EP4



Download:Ideal Coordinates CCD File
J [auth P],
U [auth A]
(1~{S},2~{S},5~{S},6~{S},8~{R},9~{S},10~{S},11~{R},15~{S},18~{R})-6,12,12-trimethyl-9,10,15,18-tetrakis(oxidanyl)-17-oxapentacyclo[7.6.2.1^{5,8}.0^{1,11}.0^{2,8}]octadecan-7-one
C20 H30 O6
RWELMBQGCLVKOE-RCARQVHKSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
E [auth P],
IA [auth C],
M [auth A]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
BA [auth B]
DA [auth B]
EA [auth B]
FA [auth B]
GA [auth C]
BA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth C],
N [auth A],
O [auth A],
OA [auth C],
V [auth A],
Y [auth B],
Z [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
ARF

Query on ARF



Download:Ideal Coordinates CCD File
AA [auth B]
CA [auth B]
F [auth P]
G [auth P]
H [auth P]
AA [auth B],
CA [auth B],
F [auth P],
G [auth P],
H [auth P],
HA [auth C],
I [auth P],
JA [auth C],
KA [auth C],
L [auth A],
LA [auth C],
MA [auth C],
NA [auth C],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
W [auth B],
X [auth B]
FORMAMIDE
C H3 N O
ZHNUHDYFZUAESO-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
K [auth P]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.282 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.235α = 90
b = 125.934β = 90
c = 132.097γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2026-07-29
    Type: Initial release
  • Version 1.1: 2026-08-12
    Changes: Database references