7WCE | pdb_00007wce

Crystal structure of HIV-1 integrase catalytic core domain in complex with (2S)-2-(tert-Butoxy)-2-(10-fluoro-2-(2-hydroxy-4-methylphenyl)-1,4-dimethyl-5-(methylsulfonyl)-5,6-dihydrophenanthridin-3-yl)acetic acid

• PDB DOI: https://doi.org/10.2210/pdb7WCE/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-12-20 Released: 2022-09-07 
• Deposition Author(s): Taoda, Y., Sekiguchi, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Discovery of tricyclic HIV-1 integrase-LEDGF/p75 allosteric inhibitors by intramolecular direct arylation reaction.

Taoda, Y., Akiyama, T., Tomita, K., Fujiwara-Kitamura, M., Tamura, Y., Kawasuji, T., Matsuoka, E., Akihisa, E., Seki, T., Yoshinaga, T.

(2022) Bioorg Med Chem Lett 64: 128664-128664

• PubMed: 35272008 
• DOI: https://doi.org/10.1016/j.bmcl.2022.128664
• Primary Citation Related Structures: 
  7WCE


• PubMed Abstract: 
  

  We have been conducting exploratory research to develop human immunodeficiency virus type-1 (HIV-1) integrase-LEDGF/p75 allosteric inhibitors (INLAIs). Here, we report on a newly designed compound with a tricyclic scaffold that shows promise as an inhibitor. Various scaffolds were synthesized by intramolecular direct arylation reaction to fix the position of a lipophilic side chain required for antiviral activity. Among these, the compound having an N-mesyl dihydrophenanthridine ring showed the best antiviral activity. Compound 42i, prepared by side chain optimization of the C-4 and C-6 positions, exhibited high antiviral activity against wild-type (WT) and the T174I mutant (EC ₅₀ (WT) = 4.6 nM, EC ₅₀ (T174I) = 83 nM) with a good PK profile. Based on co-crystal structural analysis of compound 42i and WT HIV-1 IN CCD, we discuss the interaction important for high antiviral activity.

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Organizational Affiliation: 
• Shionogi Pharmaceutical Research Center, Shionogi & Company, Limited, 1-1, Futabacho, 3-chome, Toyonaka 561-0825, Japan. Electronic address: [e-mail].
Shionogi Pharmaceutical Research Center, Shionogi & Company, Limited, 1-1, Futabacho, 3-chome, Toyonaka 561-0825, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.26 kDa 
• Atom Count: 1,217 
• Modeled Residue Count: 138 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase catalytic	A	166	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 1  EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data), 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
8Z3 (Subject of Investigation/LOI)	D [auth A]	(2S)-2-[10-fluoranyl-1,4-dimethyl-2-(4-methyl-2-oxidanyl-phenyl)-5-methylsulfonyl-6H-phenanthridin-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid C29 H32 F N O6 S CBVIAFDVGLUIGG-MHZLTWQESA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.85 Å
• R-Value Free:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.401	α = 90
b = 72.401	β = 90
c = 65.776	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Taoda, Y., Sekiguchi, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary