6NCJ | pdb_00006ncj

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 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KJJClick on this verticalbar to view details

This is version 1.2 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase180Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: pol
UniProt
Find proteins for F2WR52 (Human immunodeficiency virus type 1)
Explore F2WR52 
Go to UniProtKB:  F2WR52
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2WR52
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KJJ (Subject of Investigation/LOI)
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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.240 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
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



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KJJClick on this verticalbar to view details

Entry History 

Deposition Data

  • 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
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references