4ZTJ | pdb_00004ztj

Crystal Structure of the Prototype Foamy Virus Intasome with a 2-Pyridinone Aminal Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.221 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZTJ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance a Second Generation of HIV-1 Integrase Strand Transfer Inhibitors.

Raheem, I.T.Walji, A.M.Klein, D.Sanders, J.M.Powell, D.A.Abeywickrema, P.Barbe, G.Bennet, A.Clas, S.D.Dubost, D.Embrey, M.Grobler, J.Hafey, M.J.Hartingh, T.J.Hazuda, D.J.Miller, M.D.Moore, K.P.Pajkovic, N.Patel, S.Rada, V.Rearden, P.Schreier, J.D.Sisko, J.Steele, T.G.Truchon, J.F.Wai, J.Xu, M.Coleman, P.J.

(2015) J Med Chem 58: 8154-8165

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01037
  • Primary Citation Related Structures: 
    4ZTF, 4ZTJ

  • PubMed Abstract: 

    The search for new molecular constructs that resemble the critical two-metal binding pharmacophore required for HIV integrase strand transfer inhibition represents a vibrant area of research within drug discovery. Here we present the discovery of a new class of HIV integrase strand transfer inhibitors based on the 2-pyridinone core of MK-0536. These efforts led to the identification of two lead compounds with excellent antiviral activity and preclinical pharmacokinetic profiles to support a once-daily human dose prediction. Dose escalating PK studies in dog revealed significant issues with limited oral absorption and required an innovative prodrug strategy to enhance the high-dose plasma exposures of the parent molecules.


  • Organizational Affiliation
    • Merck Frosst Centre for Therapeutic Research , Kirkland, QC Canada.

Macromolecule Content 

  • Total Structure Weight: 101.23 kDa 
  • Atom Count: 5,324 
  • 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
PFV INTEGRASE
A, B
395Human spumaretrovirusMutation(s): 0 
Gene Names: pol
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
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')19Human spumaretrovirus
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')17Human spumaretrovirus
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4RT

Query on 4RT



Download:Ideal Coordinates CCD File
L [auth A](1R,2S,5R)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-1-(hydroxymethyl)-2'-methyl-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
C24 H23 Cl F N3 O5
CMKPKOVJKYIZNW-DHTHFVMWSA-N
SO4

Query on SO4



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

Query on GOL



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.96α = 90
b = 158.96β = 90
c = 124.47γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations