4ZTF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.5b01037
  • Structures With Same Primary Citation

  • 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 n ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrase
A, B
395Human spumaretrovirusMutation(s): 2 
Gene Names: pol
EC: 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt), 3.4.23 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P14350 (Human spumaretrovirus)
Go to UniProtKB:  P14350
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
19 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)C19Human spumaretrovirus
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
17 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)D17Human spumaretrovirus
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X2P
Query on X2P

Download CCD File 
A
(1R,2R,5S)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-2'-[(2S)-2-hydroxypropyl]-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
C25 H25 Cl F N3 O5
SUYSDXIXCVFTRC-UCVJIWRCSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.45α = 90
b = 159.45β = 90
c = 124.09γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-05-14 
  • Released Date: 2015-10-07 
  • Deposition Author(s): Klein, D.J., Patel, S.

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references