6LMQ | pdb_00006lmq

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

• PDB DOI: https://doi.org/10.2210/pdb6LMQ/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-12-26 Released: 2020-09-23 
• Deposition Author(s): Sugiyama, S., Iwaki, T., Tamura, Y., Tomita, K., Matsuoka, E., Arita, S., Seki, T., Yoshinaga, T., Kawasuji, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

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

• PubMed: 32773094 
• 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.

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Organizational Affiliation: 

Shionogi Pharmaceutical Research Center, Shionogi & Company, Limited, 1-1, Futabacho, 3-chome, Toyonaka, Osaka 561-0825, Japan. Electronic address: [e-mail].

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)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 19.34 kDa 
• Atom Count: 1,205 
• Modelled Residue Count: 143 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase catalytic	A	166	Human 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
940 (Subject of Investigation/LOI)	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	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.885	α = 90
b = 71.885	β = 90
c = 65.52	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Sugiyama, S., Iwaki, T., Tamura, Y., Tomita, K., Matsuoka, E., Arita, S., Seki, T., Yoshinaga, T., Kawasuji, T.

Revision History  

• 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