4NCG | pdb_00004ncg

Discovery of Doravirine, an orally bioavailable non-nucleoside reverse transcriptase inhibitor potent against a wide range of resistant mutant HIV viruses

• PDB DOI: https://doi.org/10.2210/pdb4NCG/pdb

• Classification: Transferase/Inhhibitor, Hydrolase/Inhhibitor
• Organism(s): HIV-1 M:B_HXB2R
• Mutation(s): Yes 


• Deposited: 2013-10-24 Released: 2014-02-12 
• Deposition Author(s): Yan, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.260 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Discovery of MK-1439, an orally bioavailable non-nucleoside reverse transcriptase inhibitor potent against a wide range of resistant mutant HIV viruses.

Cote, B., Burch, J.D., Asante-Appiah, E., Bayly, C., Bedard, L., Blouin, M., Campeau, L.C., Cauchon, E., Chan, M., Chefson, A., Coulombe, N., Cromlish, W., Debnath, S., Deschenes, D., Dupont-Gaudet, K., Falgueyret, J.P., Forget, R., Gagne, S., Gauvreau, D., Girardin, M., Guiral, S., Langlois, E., Li, C.S., Nguyen, N., Papp, R., Plamondon, S., Roy, A., Roy, S., Seliniotakis, R., St-Onge, M., Ouellet, S., Tawa, P., Truchon, J.F., Vacca, J., Wrona, M., Yan, Y., Ducharme, Y.

(2014) Bioorg Med Chem Lett 24: 917-922

• PubMed: 24412110 
• DOI: https://doi.org/10.1016/j.bmcl.2013.12.070
• Primary Citation Related Structures: 
  4NCG


• PubMed Abstract: 
  

  The optimization of a novel series of non-nucleoside reverse transcriptase inhibitors (NNRTI) led to the identification of pyridone 36. In cell cultures, this new NNRTI shows a superior potency profile against a range of wild type and clinically relevant, resistant mutant HIV viruses. The overall favorable preclinical pharmacokinetic profile of 36 led to the prediction of a once daily low dose regimen in human. NNRTI 36, now known as MK-1439, is currently in clinical development for the treatment of HIV infection.

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Organizational Affiliation: 
• Merck Frosst Centre for Therapeutic Research, 16711 Trans Canada Highway, Kirkland, Quebec H9H 3L1, Canada. Electronic address: [e-mail].
Merck Frosst Centre for Therapeutic Research, 16711 Trans Canada Highway, Kirkland, Quebec H9H 3L1, Canada.
Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, PA 19486-0004, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 117.05 kDa 
• Atom Count: 7,913 
• Modeled Residue Count: 955 
• Deposited Residue Count: 1,006 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A	563	HIV-1 M:B_HXB2R	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), 3.1.13.2 (PDB Primary Data)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p51 RT	B	443	HIV-1 M:B_HXB2R	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), 3.1.13.2 (PDB Primary Data)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2KW	C [auth A]	3-chloro-5-({1-[(4-methyl-5-oxo-4,5-dihydro-1H-1,2,4-triazol-3-yl)methyl]-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridin-3-yl}oxy)benzonitrile C17 H11 Cl F3 N5 O3 ZIAOVIPSKUPPQW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2KW	BindingDB:  4NCG	IC50: min: 19, max: 44 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.260 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.385	α = 90
b = 153.618	β = 90
c = 154.624	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Yan, Y.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2022-10-12
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-05-22
  Changes: Data collection