9L3E | pdb_00009l3e

Structure of GAPDH complexed with Leu-F

PDB DOI: https://doi.org/10.2210/pdb9L3E/pdb

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

PubMed: 40712011 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adw2578
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 149.5 kDa
Atom Count: 11,395
Modeled Residue Count: 1,336
Deposited Residue Count: 1,344
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A [auth O], B [auth P], C [auth R], D [auth Q]	336	Homo sapiens	Mutation(s): 0 Gene Names: GAPDH, GAPD, CDABP0047, OK/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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04406
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain T [auth R] SDF format, chain O [auth P] SDF format, chain J [auth O] SDF format, chain AA [auth Q] MOL2 format, chain T [auth R] MOL2 format, chain O [auth P] MOL2 format, chain J [auth O] MOL2 format, chain AA [auth Q] mmCIF format, chain T [auth R] mmCIF format, chain O [auth P] mmCIF format, chain J [auth O] mmCIF format, chain AA [auth Q]	AA [auth Q], J [auth O], O [auth P], T [auth R]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth Q] Focus chain J [auth O] Focus chain O [auth P] Focus chain T [auth R] Interactions & Density Focus chain AA [auth Q] Focus chain J [auth O] Focus chain O [auth P] Focus chain T [auth R]
A1L6Z (Subject of Investigation/LOI) Query on A1L6Z Download:Ideal Coordinates CCD File SDF format, chain E [auth O] MOL2 format, chain E [auth O] mmCIF format, chain E [auth O]	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		Interactions Focus chain E [auth O] Interactions & Density Focus chain E [auth O]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain U [auth R] SDF format, chain Q [auth P] MOL2 format, chain U [auth R] MOL2 format, chain Q [auth P] mmCIF format, chain U [auth R] mmCIF format, chain Q [auth P]	Q [auth P], U [auth R]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain Q [auth P] Focus chain U [auth R] Interactions & Density Focus chain Q [auth P] Focus chain U [auth R]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain W [auth R] SDF format, chain V [auth R] SDF format, chain P SDF format, chain K [auth O] SDF format, chain CA [auth Q] SDF format, chain BA [auth Q] MOL2 format, chain W [auth R] MOL2 format, chain V [auth R] MOL2 format, chain P MOL2 format, chain K [auth O] MOL2 format, chain CA [auth Q] MOL2 format, chain BA [auth Q] mmCIF format, chain W [auth R] mmCIF format, chain V [auth R] mmCIF format, chain P mmCIF format, chain K [auth O] mmCIF format, chain CA [auth Q] mmCIF format, chain BA [auth Q]	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		Interactions Focus chain BA [auth Q] Focus chain CA [auth Q] Focus chain K [auth O] Focus chain P Focus chain V [auth R] Focus chain W [auth R] Interactions & Density Focus chain BA [auth Q] Focus chain CA [auth Q] Focus chain K [auth O] Focus chain P Focus chain V [auth R] Focus chain W [auth R]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth Q] SDF format, chain X [auth Q] SDF format, chain R SDF format, chain M [auth P] SDF format, chain L [auth P] SDF format, chain G [auth O] SDF format, chain F [auth O] MOL2 format, chain Y [auth Q] MOL2 format, chain X [auth Q] MOL2 format, chain R MOL2 format, chain M [auth P] MOL2 format, chain L [auth P] MOL2 format, chain G [auth O] MOL2 format, chain F [auth O] mmCIF format, chain Y [auth Q] mmCIF format, chain X [auth Q] mmCIF format, chain R mmCIF format, chain M [auth P] mmCIF format, chain L [auth P] mmCIF format, chain G [auth O] mmCIF format, chain F [auth O]	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		Interactions Focus chain F [auth O] Focus chain G [auth O] Focus chain L [auth P] Focus chain M [auth P] Focus chain R Focus chain X [auth Q] Focus chain Y [auth Q] Interactions & Density Focus chain F [auth O] Focus chain G [auth O] Focus chain L [auth P] Focus chain M [auth P] Focus chain R Focus chain X [auth Q] Focus chain Y [auth Q]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth Q] SDF format, chain S [auth R] SDF format, chain N [auth P] SDF format, chain I [auth O] SDF format, chain H [auth O] MOL2 format, chain Z [auth Q] MOL2 format, chain S [auth R] MOL2 format, chain N [auth P] MOL2 format, chain I [auth O] MOL2 format, chain H [auth O] mmCIF format, chain Z [auth Q] mmCIF format, chain S [auth R] mmCIF format, chain N [auth P] mmCIF format, chain I [auth O] mmCIF format, chain H [auth O]	H [auth O], I [auth O], N [auth P], S [auth R], Z [auth Q]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth O] Focus chain I [auth O] Focus chain N [auth P] Focus chain S [auth R] Focus chain Z [auth Q] Interactions & Density Focus chain H [auth O] Focus chain I [auth O] Focus chain N [auth P] Focus chain S [auth R] Focus chain Z [auth Q]