7UOQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00115
  • Primary Citation of 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.


  • Organizational Affiliation

    ViiV Healthcare, 36 East Industrial Road, Branford, Connecticut 06405, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase180Human immunodeficiency virus 1Mutation(s): 3 
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O20 (Subject of Investigation/LOI)
Query on O20

Download Ideal Coordinates CCD File 
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
Query on SO4

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.42α = 90
b = 71.42β = 90
c = 66.654γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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