9D36 | pdb_00009d36

Structure of the C-terminal Domain of RAGE and Its Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9D36/pdb
• BMRB: 31193

• Classification: PROTEIN BINDING/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-09 Released: 2025-08-13 
• Deposition Author(s): Theophall, G.G., Ramasamy, R., Schmidt, A.M., Manigrasso, M., Shekthman, A.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10000 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

RAGE-mediated activation of the formin DIAPH1 and human macrophage inflammation are inhibited by a small molecule antagonist.

Theophall, G.G., Manigrasso, M.B., Nazarian, P., Premo, A., Reverdatto, S., Yepuri, G., Burz, D.S., Vanegas, S.M., Mangar, K., Zhao, Y., Li, H., DeVita, R.J., Ramasamy, R., Schmidt, A.M., Shekhtman, A.

(2025) Cell Chem Biol 32: 1221-1234.e8

• PubMed: 41038162 
• DOI: https://doi.org/10.1016/j.chembiol.2025.09.004
• Primary Citation Related Structures: 
  9D36


• PubMed Abstract: 
  

  RAGE and its intracellular effector molecule, the actin polymerase DIAPH1, mediate inflammation and the complications of diabetes. Using NMR spectroscopy and mass spectrometry, we built a structural model of the RAGE-DIAPH1 complex, revealing how binding of the cytoplasmic tail of RAGE (ctRAGE) to DIAPH1 stimulates its actin polymerization activity, which is inhibited by a small molecule antagonist of RAGE-DIAPH1 interaction, RAGE406R. The solution structure of the RAGE406R - ctRAGE suggests that RAGE406R prevents the formation of the RAGE-DIAPH1. FRET, actin polymerization assays, smooth muscle cell migration, and THP1 cell inflammation experiments, together with the in vivo interrogation of the effects of RAGE406R in mouse models of inflammation and diabetic wound healing, support this mode of RAGE-DIAPH1 antagonism. Finally, the treatment of macrophages differentiated from peripheral blood-derived mononuclear cells from humans with type 1 diabetes with RAGE406R reduces the mRNA expression of the chemokine CCL2, diminishing the expression of a key node in the inflammatory response.

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Organizational Affiliation: 
• Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA.
Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA.
Department of Medicine, New York Grossman School of Medicine, New York, NY 10016, USA.
Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA.
RJD Medicinal Chemistry and Drug Discovery Consulting LLC, Westfield, NJ 07091, USA.
Diabetes Research Program, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA. Electronic address: [e-mail].
Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 5.43 kDa 
• Atom Count: 186 
• Modeled Residue Count: 17 
• Deposited Residue Count: 43 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Advanced glycosylation end product-specific receptor	A	43	Homo sapiens	Mutation(s): 0  Gene Names: AGER, RAGE
UniProt & NIH Common Fund Data Resources
Find proteins for Q15109 (Homo sapiens) Explore Q15109  Go to UniProtKB:  Q15109
PHAROS:  Q15109 GTEx:  ENSG00000204305

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A2E (Subject of Investigation/LOI)	B [auth A]	4-[(morpholin-4-yl)methyl]-2-{4-[(2R)-5-oxopyrrolidin-2-yl]phenyl}quinoline-7-carbonitrile C25 H24 N4 O2 MUVCLMZDXXUHRB-JOCHJYFZSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10000 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Theophall, G.G., Ramasamy, R., Schmidt, A.M., Manigrasso, M., Shekthman, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release
  
• Version 1.1: 2026-02-25
  Changes: Database references