7U5Z | pdb_00007u5z

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with JLJ353

• PDB DOI: https://doi.org/10.2210/pdb7U5Z/pdb

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


• Deposited: 2022-03-03 Released: 2023-03-15 
• Deposition Author(s): Hollander, K., Carter, Z., Jorgensen, W.L., Anderson, K.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.280 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, and biological testing of biphenylmethyloxazole inhibitors targeting HIV-1 reverse transcriptase.

Carter, Z.J., Hollander, K., Spasov, K.A., Anderson, K.S., Jorgensen, W.L.

(2023) Bioorg Med Chem Lett 84: 129216-129216

• PubMed: 36871704 
• DOI: https://doi.org/10.1016/j.bmcl.2023.129216
• Primary Citation Related Structures: 
  7U5Z


• PubMed Abstract: 
  

  We report non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) using a biphenylmethyloxazole pharmacophore. A crystal structure of benzyloxazole 1 was obtained and suggested the potential viability of biphenyl analogues. In particular, 6a, 6b, and 7 turned out to be potent NNRTIs with low-nanomolar activity in enzyme inhibition and infected T-cell assays, and with low cytotoxicity. Though modeling further suggested that analogues with fluorosulfate and epoxide warheads might provide covalent modification of Tyr188, synthesis and testing did not find evidence for this outcome.

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Organizational Affiliation: 
• Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA.
Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA.
Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA. Electronic address: [e-mail].
Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 114.37 kDa 
• Atom Count: 7,748 
• Modeled Residue Count: 951 
• Deposited Residue Count: 985 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A	557	Human immunodeficiency virus type 1 BH10	Mutation(s): 3  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), 2.7.7 (PDB Primary Data), 3.1 (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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p51 RT	B	428	Human immunodeficiency virus type 1 BH10	Mutation(s): 1  Gene Names: gag-pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LE8 (Subject of Investigation/LOI)	C [auth A]	2-chloro-4-({5-[(2,6-difluorophenyl)methyl]-1,3-oxazol-2-yl}amino)benzonitrile C17 H10 Cl F2 N3 O XMNGPECGUKASMW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.280 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.872	α = 90
b = 73.538	β = 100.47
c = 109.226	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Hollander, K., Carter, Z., Jorgensen, W.L., Anderson, K.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH/NAD AI155072

Revision History  

• Version 1.0: 2023-03-15
  Type: Initial release
  
• Version 1.1: 2023-03-22
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description