9NLP | pdb_00009nlp

HIV-1 Reverse Transcriptase with New Non-Nucleoside Reverse Transcriptase Inhibitor 12126065


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Cryo-EM Structure of HIV-1 Reverse Transcriptase with N -Phenyl-1-(phenylsulfonyl)-1 H -1,2,4-triazol-3-amine: A New HIV-1 Non-nucleoside Inhibitor.

Young, M.A.Lane, T.R.Raman, R.Nelson, J.A.E.Riabova, O.Kazakova, E.Monakhova, N.Tsedilin, A.Rees, S.D.Quinnell, D.Makarov, V.Chang, G.Ekins, S.

(2025) ACS Infect Dis 11: 1257-1267

  • DOI: https://doi.org/10.1021/acsinfecdis.5c00189
  • Primary Citation Related Structures: 
    9NLP

  • PubMed Abstract: 

    The use of highly active antiretroviral therapy (HAART) has made the human immunodeficiency virus (HIV) a chronic disease rather than a terminal disease. Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are an important component of HAART, although we are seeing clinically relevant drug-resistant mutants such that there is a need to develop new molecules. We recently identified a new class of N -phenyl-1-(phenylsulfonyl)-1 H -1,2,4-triazol-3-amine HIV-1 NNRTI, with one known as compound 12126065, with sub nanomolar (nM) potency in TZM-bl cells (HeLa cells expressing CD4, CCR5, and CXCR4) with no in vivo acute or subacute toxicity. We now describe the cryo-EM structure of this molecule (resolution of 3.53 Å) and compare it to analogues and other known NNRTIs. We also describe the synthesis and activity of five additional analogues of this class of compounds, some of which have promising activity against a K103N/Y181C (A17) double mutant, which will enable the design of future molecules.


  • Organizational Affiliation
    • Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, San Diego, California 92093, United States.

Macromolecule Content 

  • Total Structure Weight: 117.83 kDa 
  • Atom Count: 6,052 
  • Modeled Residue Count: 726 
  • Deposited Residue Count: 1,012 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Reverse transcriptase p66 subunit571HIV-1 06TG.HT008Mutation(s): 0 
Gene Names: gag-pol
EC: 2.7.7.49
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Reverse transcriptase p51 subunit441HIV-1 06TG.HT008Mutation(s): 0 
Gene Names: gag-pol
EC: 2.7.7.49
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BYY
(Subject of Investigation/LOI)

Query on A1BYY



Download:Ideal Coordinates CCD File
C [auth A]4-({5-amino-1-[6-(2-cyanoethyl)naphthalene-1-sulfonyl]-1H-1,2,4-triazol-3-yl}amino)-2-chlorobenzonitrile
C22 H16 Cl N7 O2 S
YLHDIFMTTOCZFP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Data collection, Database references