9ONB | pdb_00009onb

Immature HIV-1 CACTD-SP1 lattice with Maturation inhibitor PF-46396 (S) and Inositol hexakisphosphate (IP6)

• PDB DOI: https://doi.org/10.2210/pdb9ONB/pdb
• BMRB: 31248

• Classification: PROTEIN BINDING
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-14 Released: 2025-10-08 
• Deposition Author(s): Zadorozhnyi, R., Quinn, C.M., Zadrozny, K.K., Ablan, S.D., Kennedy, B.J., Yap, G.P.A., Sanner, D., Kraml, C., Freed, E.O., Ganser-Pornillos, B.K., Pornillos, O., Gronenborn, A.M., Polenova, T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structural Basis for HIV-1 Maturation Inhibition by PF-46396 Determined by MAS NMR.

Zadorozhnyi, R., Quinn, C.M., Zadrozny, K.K., Ablan, S.D., Kennedy, B.J., Yap, G.P.A., Sanner, D., Kraml, C., Freed, E.O., Ganser-Pornillos, B.K., Pornillos, O., Gronenborn, A.M., Polenova, T.

(2025) J Am Chem Soc 147: 34487-34497

• PubMed: 40924873 
• DOI: https://doi.org/10.1021/jacs.5c08455
• Primary Citation Related Structures: 
  9ON8, 9ON9, 9ONA, 9ONB


• PubMed Abstract: 
  

  Among the different types of HIV-1 maturation inhibitors, those that stabilize the junction between the capsid protein C-terminal domain (CA _CTD ) and the spacer peptide 1 (SP1) within the immature Gag lattice are promising candidates for antiretroviral therapies. Here, we report the atomic-resolution structure of CA _CTD -SP1 assemblies with the small-molecule maturation inhibitor PF-46396 and the assembly cofactor inositol hexakisphosphate (IP6), determined by magic angle spinning (MAS) NMR spectroscopy. Our results reveal that although the two PF-46396 enantiomers exhibit distinct binding modes, they both possess similar anti-HIV potency. PF-46396 binding arrests IP6 dynamics in the six-helix bundle pore, and the two enantiomers induce unique IP6 orientations in the pore. Importantly, our data suggest the presence of monoanionic IP6 form in the complex. Our study establishes the structural basis for PF-46396 action and suggests a mechanistic model for drug resistance.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.
Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States.
Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States.
Center for Cancer Research, National Cancer Institute, HIV Dynamics and Replication Program, Frederick, Maryland 21702, United States.
Lotus Separations LLC, Princeton University, Princeton, New Jersey 08540, United States.
Department of Biochemistry, University of Utah Salt Lake City, Utah 84112, United States.
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 67.68 kDa 
• Atom Count: 4,707 
• Modeled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A [auth G], B [auth H], C [auth I], D [auth J], E [auth K], F [auth L]	102	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 0  Gene Names: gag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	G [auth H]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
A1CCZ (Subject of Investigation/LOI)	H	1-{(2S)-2-(4-tert-butylphenyl)-2-[(2,3-dihydro-1H-inden-2-yl)amino]ethyl}-3-(trifluoromethyl)pyridin-2(1H)-one C27 H29 F3 N2 O ARDZNPZYNMTXDH-XMMPIXPASA-N

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Zadorozhnyi, R., Quinn, C.M., Zadrozny, K.K., Ablan, S.D., Kennedy, B.J., Yap, G.P.A., Sanner, D., Kraml, C., Freed, E.O., Ganser-Pornillos, B.K., Pornillos, O., Gronenborn, A.M., Polenova, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1U54AI170791
National Science Foundation (NSF, United States)	United States	CHE0959496
National Institutes of Health/Office of the Director	United States	S10-OD026896A

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release