9B8N | pdb_00009b8n

Crystal structure of ornithine decarboxylase in complex with a novel inhibitor (10-S)

• PDB DOI: https://doi.org/10.2210/pdb9B8N/pdb

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


• Deposited: 2024-03-31 Released: 2025-03-12 
• Deposition Author(s): Schultz, C.R., Aleiwi, B., Zhou, X.E., Suino-Powell, K., Melcher, K., Brunzelle, J.S., Almeida, N.M.S., Wilson, A.K., Ellsworth, E., Bachmann, A.S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Design, Synthesis, and Biological Activity of Novel Ornithine Decarboxylase (ODC) Inhibitors.

Schultz, C.R., Aleiwi, B., Zhou, X.E., Suino-Powell, K., Melcher, K., Almeida, N.M.S., Wilson, A.K., Ellsworth, E.L., Bachmann, A.S.

(2025) J Med Chem 68: 5760-5773

• PubMed: 40035393 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c03120
• Primary Citation of Related Structures:  
  9B8M, 9B8N


• PubMed Abstract: 
  

  We here describe the design, synthesis, and biological activity of novel ornithine decarboxylase (ODC) inhibitors that show significantly higher potency in vitro than α-difluoromethylornithine (DFMO), a U.S. Food and Drug Administration (FDA) approved drug. We report two X-ray structures of ODC complexed with new ODC inhibitors, computational docking, molecular dynamics, and binding free energy calculations to validate the experimental models. The X-ray structures reveal that covalent adducts with pyridoxal phosphate (PLP) are formed in the active site of the human ODC enzyme, as verified by their preparation and enzymatic testing. Finally, we verified that the cellular activity of endogenous ODC was inhibited, and polyamine levels were reduced. Given that ODC is a clinically validated target, combined with the fact that DFMO is currently the only ODC inhibitor in clinical use for several indications, the further development of more potent ODC inhibitors with superior activity and physical properties is warranted.

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Organizational Affiliation: 
• Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan 49503, United States.
International Center for Polyamine Disorders, Grand Rapids, Michigan 49503, United States.
Department of Pharmacology and Toxicology, College of Human Medicine, East Lansing, Michigan 48824, United States.
Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States.
Department of Chemistry, College of Natural Science, Michigan State University, East Lansing, Michigan 48824, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 95.21 kDa 
• Atom Count: 7,009 
• Modeled Residue Count: 817 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine decarboxylase	A, B	424	Homo sapiens	Mutation(s): 0  Gene Names: ODC1 EC: 4.1.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P11926 (Homo sapiens) Explore P11926  Go to UniProtKB:  P11926
PHAROS:  P11926 GTEx:  ENSG00000115758

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
A1AQP (Subject of Investigation/LOI)	D [auth A], F [auth B]	O-{[(3S)-pyrrolidin-3-yl]methyl}hydroxylamine C5 H12 N2 O ZTLUVRQAZGGKNA-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.34	α = 90
b = 87.36	β = 90
c = 154.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Schultz, C.R., Aleiwi, B., Zhou, X.E., Suino-Powell, K., Melcher, K., Brunzelle, J.S., Almeida, N.M.S., Wilson, A.K., Ellsworth, E., Bachmann, A.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R21 CA216867

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Database references