6NCJ | pdb_00006ncj

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.

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

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

PubMed: 30609350 Search on PubMed
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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 type 1) Explore F2WR52 Go to UniProtKB: F2WR52
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F2WR52
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KJJ (Subject of Investigation/LOI) Query on KJJ Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	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		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]