5UOP | pdb_00005uop

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 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5UOP

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmcl.2017.02.039
  • Primary Citation Related Structures: 
    5UOP, 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 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.

Macromolecule Content 

  • Total Structure Weight: 101.4 kDa 
  • Atom Count: 5,333 
  • Modeled Residue Count: 588 
  • Deposited Residue Count: 826 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INTEGRASE
A, B
395Human spumaretrovirusMutation(s): 2 
Gene Names: pol
EC: 2.7.7
UniProt
Find proteins for P14350 (Human spumaretrovirus)
Explore P14350 
Go to UniProtKB:  P14350
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14350
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)19Human spumaretrovirus
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)17Human spumaretrovirus
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8G4

Query on 8G4



Download:Ideal Coordinates CCD File
M [auth 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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
L [auth A],
O [auth B],
Q [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
P [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.203 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.818α = 90
b = 158.818β = 90
c = 123.797γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations