6NCJ

Structure of HIV-1 Integrase with potent 5,6,7,8-Tetrahydro-1,6-naphthyridine Derivatives Allosteric Site Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

5,6,7,8-Tetrahydro-1,6-naphthyridine Derivatives as Potent HIV-1-Integrase-Allosteric-Site Inhibitors.

Peese, K.M.Allard, C.W.Connolly, T.Johnson, B.L.Li, C.Patel, M.Sorensen, M.E.Walker, M.A.Meanwell, N.A.McAuliffe, B.Minassian, B.Krystal, M.Parker, D.D.Lewis, H.A.Kish, K.Zhang, P.Nolte, R.T.Simmermacher, J.Jenkins, S.Cianci, C.Naidu, B.N.

(2019) J Med Chem 62: 1348-1361

  • DOI: 10.1021/acs.jmedchem.8b01473
  • Primary Citation of Related Structures:  
    6NCJ

  • PubMed Abstract: 
  • A series of 5,6,7,8-tetrahydro-1,6-naphthyridine derivatives targeting the allosteric lens-epithelium-derived-growth-factor-p75 (LEDGF/p75)-binding site on HIV-1 integrase, an attractive target for antiviral chemotherapy, was prepared and screened for activity against HIV-1 infection in cell culture ...

    A series of 5,6,7,8-tetrahydro-1,6-naphthyridine derivatives targeting the allosteric lens-epithelium-derived-growth-factor-p75 (LEDGF/p75)-binding site on HIV-1 integrase, an attractive target for antiviral chemotherapy, was prepared and screened for activity against HIV-1 infection in cell culture. Small molecules that bind within the LEDGF/p75-binding site promote aberrant multimerization of the integrase enzyme and are of significant interest as HIV-1-replication inhibitors. Structure-activity-relationship studies and rat pharmacokinetic studies of lead compounds are presented.


    Organizational Affiliation

    Protein Cellular and Structural Sciences , GlaxoSmithKline , 1250 South Collegeville Rd. , Collegeville , Pennsylvania 19426 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseA180Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: pol
UniProt
Find proteins for F2WR52 (Human immunodeficiency virus 1)
Explore F2WR52 
Go to UniProtKB:  F2WR52
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KJJ
Query on KJJ

Download Ideal Coordinates CCD File 
F [auth A](2~{S})-2-[4-(8-fluoranyl-5-methyl-3,4-dihydro-2~{H}-chromen-6-yl)-2-methyl-6-[[(1~{S},2~{R})-2-phenylcyclopropyl]methyl]-7,8-dihydro-5~{H}-1,6-naphthyridin-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid
C35 H41 F N2 O4
BXDYSLFANINKPQ-VEWAMZQOSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KJJIC50:  24   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.29α = 90
b = 72.29β = 90
c = 64.79γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-12-11 
  • Released Date: 2019-01-16 
  • Deposition Author(s): Nolte, R.T.

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references