8V17 | pdb_00008v17

HIV-CA Disulfide linked Hexamer with inhibitor bound - exploration of a benzothiazole

• PDB DOI: https://doi.org/10.2210/pdb8V17/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-19 Released: 2024-12-11 
• Deposition Author(s): Goldstone, D.C., Walsham, L.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.142 (DCC) 

Starting Model: experimental

Literature

"Pseudosubstrate Envelope"/Free Energy Perturbation-Guided Design and Mechanistic Investigations of Benzothiazole HIV Capsid Modulators with High Ligand Efficiency.

Xu, S., Wang, S., Zhou, Y., Foley, N., Sun, L., Walsham, L., Tang, K., Shi, D., Shi, X., Zhang, Z., Jiang, X., Gao, S., Liu, X., Pannecouque, C., Goldstone, D.C., Dick, A., Zhan, P.

(2024) J Med Chem 67: 19057-19076

• PubMed: 39418501 
• DOI: https://doi.org/10.1021/acs.jmedchem.4c01544
• Primary Citation Related Structures: 
  8V17


• PubMed Abstract: 
  

  Based on our proposed "pseudosubstrate envelope" concept, 25 benzothiazole-bearing HIV capsid protein (CA) modulators were designed and synthesized under the guidance of free energy perturbation technology. The most potent compound, IC-1k , exhibited an EC ₅₀ of 2.69 nM against HIV-1, being 393 times more potent than the positive control PF74. Notably, IC-1k emerged as the highest ligand efficiency (LE = 0.32) HIV CA modulator, surpassing that of the approved drug lenacapavir (LE = 0.21). Surface plasmon resonance assay and crystallographic analysis confirmed that IC-1k targeted HIV-1 CA within the chemical space of the "pseudosubstrate envelope". Further mechanistic studies revealed a dual-stage inhibition profile: IC-1k disrupted early-stage capsid-host-factor interactions and promoted late-stage capsid misassembly. Preliminary pharmacokinetic evaluations demonstrated significantly improved metabolic stability in human liver microsomes for IC-1k ( T _1/2 = 91.3 min) compared to PF74 ( T _1/2 = 0.7 min), alongside a favorable safety profile. Overall, IC-1k presents a promising lead compound for further optimization.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, PR China.
Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States.
School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand.
Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), Leuven B-3000, Belgium.

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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.05 kDa 
• Atom Count: 1,921 
• Modeled Residue Count: 219 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spacer peptide 1	A	229	Human immunodeficiency virus 1	Mutation(s): 4  Gene Names: gag
UniProt
Find proteins for Q72497 (Human immunodeficiency virus type 1) Explore Q72497  Go to UniProtKB:  Q72497

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y4X (Subject of Investigation/LOI)	B [auth A]	N-(1,3-benzothiazol-5-yl)-3,5-difluoro-Nalpha-[(5-hydroxy-1H-indol-3-yl)acetyl]-N-methyl-L-phenylalaninamide C27 H22 F2 N4 O3 S ZEQNNGUVENPVCM-XMMPIXPASA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.142 (DCC) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.902	α = 90
b = 90.902	β = 90
c = 56.468	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Goldstone, D.C., Walsham, L.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release