9L3E | pdb_00009l3e

Structure of GAPDH complexed with Leu-F

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-12-18 Released: 2025-08-06 
  • Deposition Author(s): Gong, L.
  • Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.211 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Plant defense-directed discovery of a natural anti-psoriasis agent targeting GAPDH.

Zhou, T.T.Zheng, Y.Zhang, M.W.Gong, L.H.Guo, K.He, X.P.Liu, Y.C.Gershenzon, J.Liu, Y.Li, S.H.

(2025) Sci Adv 11: eadw2578-eadw2578

  • DOI: https://doi.org/10.1126/sciadv.adw2578
  • Primary Citation of Related Structures:  
    9L3E

  • PubMed Abstract: 

    Elucidating the ecological functions of natural products in plant adaptive mechanisms is an emerging means of discovering lead compounds. Here, we show an undescribed plant glandular trichome-specific defense sesterterpenoid, leucosceptrine F (leu-F), exhibiting potent anti-inflammatory activity by modulating both innate and adaptive immune responses. Leu-F irreversibly binds to glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a cross-kingdom glycolytic enzyme and a promising therapeutic target in autoimmune diseases. Crystal structure of the GAPDH-leu-F complex reveals the formation of a covalent bond between leu-F and the Cys 152 residue. Leu-F notably attenuated glycolysis and concurrently diminished GAPDH-mediated stabilization of activated protein kinase B (AKT). Both leu-F and the total sesterterpenoid extract of Leucosceptrum canum demonstrated notable therapeutic efficacy and safety in mouse models of psoriasis and experimental autoimmune encephalomyelitis. This study underscores leu-F as a promising lead compound for autoimmune disease treatment and provides a compelling example of drug discovery inspired by chemical ecology.


  • Organizational Affiliation
    • State Key Laboratory of Phytochemistry and Natural Medicines, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenaseA [auth O],
B [auth P],
C [auth R],
D [auth Q]
336Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
AA [auth Q],
J [auth O],
O [auth P],
T [auth R]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
A1L6Z (Subject of Investigation/LOI)
Query on A1L6Z

Download Ideal Coordinates CCD File 
E [auth O](4~{a}~{S},5~{S},5~{a}~{R},6~{S},8~{a}~{R},9~{S},9~{a}~{S})-3,6,9-trimethyl-5-[(1~{S},2~{R})-2-methyl-4-(3-methylfuran-2-yl)-1-oxidanyl-butyl]-3,4,5~{a},6,7,8,8~{a},9-octahydro-2~{H}-cyclopenta[g]chromene-4~{a},5,9~{a}-triol
C25 H40 O6
NYTILQADEOYMMD-POWAAIPISA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
Q [auth P],
U [auth R]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth Q]
CA [auth Q]
K [auth O]
P
V [auth R]
BA [auth Q],
CA [auth Q],
K [auth O],
P,
V [auth R],
W [auth R]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth O]
G [auth O]
L [auth P]
M [auth P]
R
F [auth O],
G [auth O],
L [auth P],
M [auth P],
R,
X [auth Q],
Y [auth Q]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth O],
I [auth O],
N [auth P],
S [auth R],
Z [auth Q]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.211 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.26α = 90
b = 133.02β = 90
c = 146.02γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MR-Rosettaphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-08-06 
  • Deposition Author(s): Gong, L.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release