6LMQ image
Deposition Date 2019-12-26
Release Date 2020-09-23
Last Version Date 2024-10-16
Entry Detail
PDB ID:
6LMQ
Keywords:
TRANSFERASE
Title:
Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-[3-(3,4-dihydro-2H-1,4-benzoxazin-6-yl)-6-methanesulfonamido-2,3',4',5-tetramethyl-[1,1'-biphenyl]-4-yl]acetic acid
Biological Source:
Source Organism:
Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (Taxon ID: 11698)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.10 Å
R-Value Free:
0.23
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 31 2 1
6LMQ validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Integrase catalytic
Gene (Uniprot):gag-pol
Mutations:F185K
Chain IDs:A
Chain Length:166
Number of Molecules:1
Biological Source:Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
UniProt ID:P12497 Pfam ID:PF00665
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CAF A CYS modified residue
Ligand Molecules
940
PGE
SO4
Primary Citation
Discovery of novel integrase-LEDGF/p75 allosteric inhibitors based on a benzene scaffold.
Bioorg.Med.Chem. 28 115643 115643 (2020)
PMID: 32773094 DOI: 10.1016/j.bmc.2020.115643

Abstact

We report herein the discovery of novel integrase-LEDGF/p75 allosteric inhibitors (INLAIs) based on a benzene scaffold 3. This scaffold can extend substituents from the C1 position unlike the common pyridine scaffolds 2. Structure-activity relationship studies showed that the sulfonamide linker at the C1 position was important for the antiviral activity. Interaction between sulfonamide and Q95 was observed by X-ray crystallography. Compound 31h showed more potent antiviral activity (EC50 (NL432) = 3.9 nM) than BI-224436 (EC50 (NL432) = 56 nM), suggesting the potential of the newly designed scaffold 3.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6LMI