7UOQ | pdb_00007uoq

CRYSTAL STRUCTURE OF HIV-1 INTEGRASE COMPLEXED WITH (2S)-2-(TERT-BUTOXY)-2-(5-{2-[(2-CHLORO-6-M ETHYLPHENYL)METHYL]-1,2,3,4-TETRAHYDROISOQUINOLIN-6-YL}-4- (4,4-DIMETHYLPIPERIDIN-1-YL)-2-METHYLPYRIDIN-3-YL)ACETIC ACID

• PDB DOI: https://doi.org/10.2210/pdb7UOQ/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2022-04-13 Released: 2022-07-06 
• Deposition Author(s): Lewis, H.A., Muckelbauer, J.K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.224 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Discovery and Preclinical Profiling of GSK3839919, a Potent HIV-1 Allosteric Integrase Inhibitor.

Parcella, K., Wang, T., Eastman, K., Zhang, Z., Yin, Z., Patel, M., Tu, Y., Zheng, B.Z., Walker, M.A., Saulnier, M.G., Frennesson, D., Bowsher, M., Gillis, E., Peese, K., Belema, M., Cianci, C., Dicker, I.B., McAuliffe, B., Ding, B., Falk, P., Simmermacher, J., Parker, D.D., Sivaprakasam, P., Kish, K., Lewis, H., Hanumegowda, U., Jenkins, S., Kadow, J.F., Krystal, M., Meanwell, N.A., Naidu, B.N.

(2022) ACS Med Chem Lett 13: 972-980

• PubMed: 35707159 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00115
• Primary Citation Related Structures: 
  7UOQ


• PubMed Abstract: 
  

  Allosteric HIV-1 integrase inhibitors (ALLINIs) have been of interest recently because of their novel mechanism of action. Strategic modifications to the C5 moiety of a class of 4-(4,4-dimethylpiperidinyl)-2,6-dimethylpyridinyl ALLINIs led to the identification of a tetrahydroisoquinoline heterocycle as a suitable spacer element to project the distal hydrophobic aryl ring. Subsequent optimization of the aryl substitutions identified 12 as an ALLINI with single-digit nanomolar inhibitory potency and low clearance across preclinical species. In preclinical toxicology studies with 12 in rats, lipid hepatocellular vacuolation was observed. Removal of the C6 methyl group resulted in GSK3839919 ( 22 ), which exhibited a reduced incidence and severity of lipid vacuolation in both in vitro assays and in vivo studies while maintaining the potency and pharmacokinetic (PK) properties of the prototype. The virology, PK, and toxicology profiles of 22 are discussed.

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Organizational Affiliation: 
• ViiV Healthcare, 36 East Industrial Road, Branford, Connecticut 06405, United States.
Research and Early Development, Bristol Myers Squibb, P.O. Box 4000, Princeton, New Jersey 08543-4000, 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: 20.58 kDa 
• Atom Count: 1,160 
• Modeled Residue Count: 140 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	180	Human immunodeficiency virus 1	Mutation(s): 3
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
O20 (Subject of Investigation/LOI)	B [auth A]	(2S)-tert-butoxy[(5M)-5-{2-[(2-chloro-6-methylphenyl)methyl]-1,2,3,4-tetrahydroisoquinolin-6-yl}-4-(4,4-dimethylpiperidin-1-yl)-2-methylpyridin-3-yl]acetic acid C36 H46 Cl N3 O3 KETKYQCQNXUIQX-XIFFEERXSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.224 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.42	α = 90
b = 71.42	β = 90
c = 66.654	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Lewis, H.A., Muckelbauer, J.K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2024-02-14
  Changes: Data collection