6LMI | pdb_00006lmi

Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-6-methanesulfonamido-2,3',4',5-tetramethyl-[1,1'-biphenyl]-4-yl]acetic acid

PDB DOI: https://doi.org/10.2210/pdb6LMI/pdb

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

Deposited: 2019-12-25 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.244 (Depositor), 0.253 (DCC)
R-Value Work:
0.197 (Depositor), 0.201 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 32773094 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2020.115643
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 19.4 kDa
Atom Count: 1,154
Modeled Residue Count: 141
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EJ9 (Subject of Investigation/LOI) Query on EJ9 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(2S)-2-[2-(3,4-dihydro-2H-chromen-6-yl)-4-(3,4-dimethylphenyl)-3,6-dimethyl-5-(methylsulfonylamino)phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid C₃₂ H₃₉ N O₆ S LTSGKVBEKJSHBH-PMERELPUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.244 (Depositor), 0.253 (DCC)
R-Value Work: 0.197 (Depositor), 0.201 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.926	α = 90
b = 71.926	β = 90
c = 65.798	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

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: 2024-11-06
Changes: Structure summary