8ZHA | pdb_00008zha

HIV-1 integrase core domain in complex with compound 15

• PDB DOI: https://doi.org/10.2210/pdb8ZHA/pdb

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


• Deposited: 2024-05-10 Released: 2024-07-10 
• Deposition Author(s): Furuzono, T., Orita, T., Nomura, A., Adachi, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.211 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Design and synthesis of novel and potent allosteric HIV-1 integrase inhibitors with a spirocyclic moiety.

Adachi, K., Manabe, T., Yamasaki, T., Suma, A., Orita, T., Furuzono, T., Adachi, T., Ohata, Y., Akiyama, Y., Miyazaki, S.

(2024) Bioorg Med Chem Lett 110: 129864-129864

• PubMed: 38942126 
• DOI: https://doi.org/10.1016/j.bmcl.2024.129864
• Primary Citation Related Structures: 
  8ZH4, 8ZHA


• PubMed Abstract: 
  

  We report herein the design and discovery of novel allosteric HIV-1 integrase inhibitors. Our design concept utilized the spirocyclic moiety to restrain the flexibility of the conformation of the lipophilic part of the inhibitor. Compound 5 showed antiviral activity by binding to the nuclear lens epithelium-derived growth factor (LEDGF/p75) binding site of HIV-1 integrase (IN). The introduction of a lipophilic amide substituent into the central benzene ring resulted in a significant increase in antiviral activity against HIV-1 WT X-ray crystallography of compound 15 in complex with the integrase revealed the presence of a hydrogen bond between the oxygen atom of the amide of compound 15 and the hydroxyl group of the T125 side chain. Chiral compound 17 showed high antiviral activity, good bioavailability, and low clearance in rats.

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Organizational Affiliation: 
• Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan. Electronic address: [e-mail].
Innovation to Implementation Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
Department of Research Planning, Preclinical, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
DMPK Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.43 kDa 
• Atom Count: 1,257 
• Modeled Residue Count: 143 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	166	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L1W	C [auth A]	(2~{S})-2-[7-(cycloheptylcarbamoyl)-4',5-dimethyl-spiro[1,2-dihydroindene-3,1'-cyclohexane]-4-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid C30 H45 N O4 OJRZALXVPTWGHE-ZLGRQJJPSA-N
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.211 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.74	α = 90
b = 72.74	β = 90
c = 66.45	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Furuzono, T., Orita, T., Nomura, A., Adachi, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Structure summary