4WE1

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-2-naphthonitrile (JLJ600)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

Starting Model: experimental
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Literature

Picomolar Inhibitors of HIV-1 Reverse Transcriptase: Design and Crystallography of Naphthyl Phenyl Ethers.

Lee, W.G., Frey, K.M., Gallardo-Macias, R., Spasov, K.A., Bollini, M., Anderson, K.S., Jorgensen, W.L.

(2014) ACS Med Chem Lett 5: 1259-1262

  • DOI: https://doi.org/10.1021/ml5003713
  • Primary Citation of Related Structures:  
    4WE1

  • PubMed Abstract: 

    Catechol diethers that incorporate a 6-cyano-1-naphthyl substituent have been explored as non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs). Promising compounds are reported that show midpicomolar activity against the wild-type virus and sub-20 nM activity against viral variants bearing Tyr181Cys and Lys103Asn mutations in HIV-RT. An X-ray crystal structure at 2.49 Å resolution is also reported for the key compound 6e with HIV-RT.

    • Organizational Affiliation: 

    Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag-Pol polyprotein557Human immunodeficiency virus type 1 BH10Mutation(s): 3 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 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 P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gag-Pol polyprotein428Human immunodeficiency virus type 1 BH10Mutation(s): 1 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 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 P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3LQ
Query on 3LQ
Download Ideal Coordinates CCD File 
C [auth A]5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}naphthalene-2-carbonitrile
C23 H17 N3 O4
OGMGBCQZVDVHAE-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.271α = 90
b = 67.218β = 108.08
c = 102.483γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI104334
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM49551
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI44616
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM32136

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description