6LMQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of novel integrase-LEDGF/p75 allosteric inhibitors based on a benzene scaffold.

Sugiyama, S.Iwaki, T.Tamura, Y.Tomita, K.Matsuoka, E.Arita, S.Seki, T.Yoshinaga, T.Kawasuji, T.

(2020) Bioorg Med Chem 28: 115643-115643

  • DOI: https://doi.org/10.1016/j.bmc.2020.115643
  • Primary Citation of Related Structures:  
    6LMI, 6LMQ

  • PubMed Abstract: 

    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 (EC 50 (NL432) = 3.9 nM) than BI-224436 (EC 50 (NL432) = 56 nM), suggesting the potential of the newly designed scaffold 3.


  • Organizational Affiliation

    Shionogi Pharmaceutical Research Center, Shionogi & Company, Limited, 1-1, Futabacho, 3-chome, Toyonaka, Osaka 561-0825, Japan. Electronic address: shuichi.sugiyama@shionogi.co.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase catalytic166Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 1 
EC: 2.7.7
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
940 (Subject of Investigation/LOI)
Query on 940

Download Ideal Coordinates CCD File 
E [auth A](2S)-2-[2-(3,4-dihydro-2H-1,4-benzoxazin-6-yl)-4-(3,4-dimethylphenyl)-3,6-dimethyl-5-(methylsulfonylamino)phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid
C31 H38 N2 O6 S
FNYNJPVNHSXBIJ-LJAQVGFWSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
D [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CAF
Query on CAF
A
L-PEPTIDE LINKINGC5 H12 As N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.885α = 90
b = 71.885β = 90
c = 65.52γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary