9DM9 | pdb_00009dm9

HIV-RT pre-catalytic complex with MK-8527


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 
    0.228 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

MK-8527 is a novel inhibitor of HIV-1 reverse transcriptase translocation with potential for extended-duration dosing.

Raheem, I.T.Girijavallabhan, V.Fillgrove, K.L.Goh, S.L.Bahnck-Teets, C.Huang, Q.Li, F.Wan, B.L.O'Donnell, G.T.Patteson, J.B.Cilento, M.E.Bennet, A.Hayes, R.P.Tummala, S.McHale, C.Wiltsie, J.Ellis, J.Asante-Appiah, E.Hazuda, D.J.Hale, J.Grobler, J.A.Xu, M.Diamond, T.L.Lai, M.T.

(2025) PLoS Biol 23: e3003308-e3003308

  • DOI: https://doi.org/10.1371/journal.pbio.3003308
  • Primary Citation Related Structures: 
    9DM9

  • PubMed Abstract: 

    Nucleoside reverse transcriptase translocation inhibitors (NRTTIs) are potent antiretroviral agents that block HIV replication. A comprehensive lead optimization campaign was undertaken to develop a novel long-acting NRTTI with the potential for extended-duration dosing for HIV prophylaxis. Broad exploration of nucleoside structure-activity relationship (SAR), leveraging ribose core, periphery, and nucleobase modifications, along with systematic progression of compounds of interest through key in vitro and in vivo studies led to the discovery of MK-8527. MK-8527 is a novel deoxyadenosine analog that is phosphorylated intracellularly to its active triphosphate (TP) form, which inhibits reverse transcription. Iron footprinting and primer extension assays demonstrated that MK-8527-TP inhibits translocation of reverse transcriptase on the primer and template, and this inhibition allows for both immediate and delayed chain termination of reverse transcription. MK-8527 inhibits viral replication in human peripheral blood mononuclear cells (PBMCs), with a half maximal inhibitory concentration (IC50) of 0.21 nM. The pharmacokinetic (PK) profile of MK-8527 in rats and rhesus monkeys was characterized by low-to-moderate clearance and volume of distribution, with good oral absorption (57% and 100% in rats and monkeys, respectively). Following oral administration of MK-8527 to monkeys, MK-8527-TP exhibited an intracellular half-life of approximately 48 h in PBMCs, significantly longer than the apparent plasma half-life of the parent compound (approximately 7 h). MK-8527 and MK-8527-TP demonstrated favorable in vitro off-target profiles, with IC50 values of ≥95 µM against human DNA polymerases tested, and no off-target activities at 10 μM against a panel of 114 enzyme and receptor binding assays. Collectively, the potent antiretroviral activity and favorable preclinical PK and off-target profiles make MK-8527 an attractive clinical candidate, and it is currently in clinical trials for once-monthly oral HIV-1 pre-exposure prophylaxis.


  • Organizational Affiliation
    • Merck & Co., Inc., Rahway, New Jersey, United States of America.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse transcriptase/ribonuclease H562HIV-1 M:B_HXB2RMutation(s): 2 
Gene Names: gag-pol
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
p51 RT455HIV-1 M:B_HXB2RMutation(s): 1 
Gene Names: gag-pol
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA PrimerC [auth P]21synthetic construct
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA TemplateD [auth T]27synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A6R (Subject of Investigation/LOI)
Query on A1A6R

Download Ideal Coordinates CCD File 
F [auth A]2-chloro-7-{(4xi)-2-deoxy-4-ethynyl-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine
C13 H16 Cl N4 O12 P3
NQMWULQTTWGPJA-IGJMFERPSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free:  0.228 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.906α = 90
b = 170.81β = 90
c = 101.453γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Database references