5UOP

CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2- PYRIDINONE AMINAL INHIBITOR (COMPOUND 18)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV.

Schreier, J.D.Embrey, M.W.Raheem, I.T.Barbe, G.Campeau, L.C.Dubost, D.McCabe Dunn, J.Grobler, J.Hartingh, T.J.Hazuda, D.J.Klein, D.Miller, M.D.Moore, K.P.Nguyen, N.Pajkovic, N.Powell, D.A.Rada, V.Sanders, J.M.Sisko, J.Steele, T.G.Wai, J.Walji, A.Xu, M.Coleman, P.J.

(2017) Bioorg. Med. Chem. Lett. 27: 2038-2046

  • DOI: 10.1016/j.bmcl.2017.02.039
  • Primary Citation of Related Structures:  5UOQ

  • PubMed Abstract: 
  • HIV integrase strand transfer inhibitors (InSTIs) represent an important class of antiviral therapeutics with proven efficacy and excellent tolerability for the treatment of HIV infections. In 2007, Raltegravir became the first marketed strand transf ...

    HIV integrase strand transfer inhibitors (InSTIs) represent an important class of antiviral therapeutics with proven efficacy and excellent tolerability for the treatment of HIV infections. In 2007, Raltegravir became the first marketed strand transfer inhibitor pioneering the way to a first-line therapy for treatment-naïve patients. Challenges with this class of therapeutics remain, including frequency of the dosing regimen and the genetic barrier to resistance. To address these issues, research towards next-generation integrase inhibitors has focused on imparting potency against RAL-resistent mutants and improving pharmacokinetic profiles. Herein, we detail medicinal chemistry efforts on a novel class of 2-pyridinone aminal InSTIs, inpsired by MK-0536, which led to the discovery of important lead molecules for our program. Systematic optimization carried out at the amide and aminal positions on the periphery of the core provided the necessary balance of antiviral activity and physiochemical properties. These efforts led to a novel aminal lead compound with the desired virological profile and preclinical pharmacokinetic profile to support a once-daily human dose prediction.


    Organizational Affiliation

    Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States. Electronic address: john_schreier@merck.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTEGRASE
A, B
395Human spumaretrovirusGene Names: pol
EC: 3.1.26.4, 3.1.-.-, 2.7.7.49, 2.7.7.7, 2.7.7.-, 3.4.23.-
Find proteins for P14350 (Human spumaretrovirus)
Go to UniProtKB:  P14350
Entity ID: 2
MoleculeChainsLengthOrganism
NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)C19Human spumaretrovirus
Entity ID: 3
MoleculeChainsLengthOrganism
NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)D17Human spumaretrovirus
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
8G4
Query on 8G4

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Download CCD File 
A
(1S,2S,5R)-8'-[(3-chloro-4-fluorophenyl)methyl]-2'-[2-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)ethyl]-6'-hydroxy-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione
C28 H24 Cl F N4 O6
PTJSQLXTSPVZSQ-AFRUXQHESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 158.818α = 90.00
b = 158.818β = 90.00
c = 123.797γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-02-01 
  • Released Date: 2017-03-29 
  • Deposition Author(s): Klein, D.J.

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-19
    Type: Database references