2YKN | pdb_00002ykn

Crystal structure of HIV-1 Reverse Transcriptase (RT) in complex with a Difluoromethylbenzoxazole (DFMB) Pyrimidine Thioether derivative, a non-nucleoside RT inhibitor (NNRTI)

PDB DOI: https://doi.org/10.2210/pdb2YKN/pdb

Classification: HYDROLASE
Organism(s): Human immunodeficiency virus type 1 BH10
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-05-28 Released: 2011-08-17
Deposition Author(s): Boyer, J., Arnoult, E., Medebielle, M., Guillemont, J., Unge, T., Unge, J., Jochmans, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.279 (Depositor), 0.279 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Difluoromethylbenzoxazole Pyrimidine Thioether Derivatives: A Novel Class of Potent Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors.

Boyer, J., Arnoult, E., Medebielle, M., Guillemont, J., Unge, J., Jochmans, D.

(2011) J Med Chem 54: 7974

PubMed: 22017513 Search on PubMed
DOI: https://doi.org/10.1021/jm200766b
Primary Citation Related Structures:
2YKM, 2YKN

PubMed Abstract:
This paper reports the synthesis and antiviral properties of new difluoromethylbenzoxazole (DFMB) pyrimidine thioether derivatives as non-nucleoside HIV-1 reverse transcriptase inhibitors. By use of a combination of structural biology study and traditional medicinal chemistry, several members of this novel class were synthesized using a single electron transfer chain process (radical nucleophilic substitution, S(RN)1) and were found to be potent against wild-type HIV-1 reverse transcriptase, with low cytotoxicity but with moderate activity against drug-resistant strains. The most promising compound 24 showed a significant EC(50) value close to 6.4 nM against HIV-1 IIIB, a moderate EC(50) value close to 54 μM against an NNRTI resistant double mutant (K103N + Y181C), but an excellent selectivity index >15477 (CC(50) > 100 μM).

Organizational Affiliation

Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR CNRS-UCBL-INSA, Equipe Synthèse de Molécules d'Intérêt Thérapeutique, Bâtiment Curien, 43 Boulevard du 11 Novembre 1918, F-69622 Villeurbanne, France.

Macromolecule Content

Total Structure Weight: 115.16 kDa
Atom Count: 8,192
Modeled Residue Count: 969
Deposited Residue Count: 990
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE/RIBONUCLEASE H	A	562	Human immunodeficiency virus type 1 BH10	Mutation(s): 2 EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE/RIBONUCLEASE H	B	428	Human immunodeficiency virus type 1 BH10	Mutation(s): 0 EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YKN Query on YKN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-[DIFLUORO-[(4-METHYL-PYRIMIDINYL)-THIO]METHYL]-BENZOXAZOLE C₁₃ H₉ F₂ N₃ O S VJAIXDQDRKEAAZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.279 (Depositor), 0.279 (DCC)
R-Value Work: 0.227 (Depositor), 0.227 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.046	α = 90
b = 155.576	β = 90
c = 152.764	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-08-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-17
Type: Initial release
Version 1.1: 2011-12-14
Changes: Database references
Version 1.2: 2018-01-17
Changes: Data collection
Version 1.3: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description