6NCJ

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

• PDB DOI: https://doi.org/10.2210/pdb6NCJ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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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 

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

• PubMed: 30609350 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.7 kDa 
• Atom Count: 1,259 
• Modelled Residue Count: 142 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	180	Human immunodeficiency virus 1	Mutation(s): 3  Gene Names: pol
UniProt
Find proteins for F2WR52 (Human immunodeficiency virus 1) Explore F2WR52  Go to UniProtKB:  F2WR52

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KJJ (Subject of Investigation/LOI)	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	G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KJJ	Binding MOAD:  6NCJ	IC50: 24 (nM) from 1 assay(s)

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 = 72.29	α = 90
b = 72.29	β = 90
c = 64.79	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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