6AOC | pdb_00006aoc

Crystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase

• PDB DOI: https://doi.org/10.2210/pdb6AOC/pdb

• Classification: TRANSFERASE / TRANSFERASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-08-15 Released: 2018-08-08 
• Deposition Author(s): Kirby, K.A., Sarafianos, S.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H.

Kankanala, J., Kirby, K.A., Huber, A.D., Casey, M.C., Wilson, D.J., Sarafianos, S.G., Wang, Z.

(2017) Eur J Med Chem 141: 149-161

• PubMed: 29031062 
• DOI: https://doi.org/10.1016/j.ejmech.2017.09.054
• Primary Citation Related Structures: 
  6AOC


• PubMed Abstract: 
  

  Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only HIV enzymatic function not targeted by current antiviral drugs. Although various chemotypes have been reported to inhibit HIV RNase H, few have shown significant antiviral activities. We report herein the design, synthesis and biological evaluation of a novel N-hydroxy thienopyrimidine-2,3-dione chemotype (11) which potently and selectively inhibited RNase H with considerable potency against HIV-1 in cell culture. Current structure-activity-relationship (SAR) identified analogue 11d as a nanomolar inhibitor of RNase H (IC ₅₀  = 0.04 μM) with decent antiviral potency (EC ₅₀  = 7.4 μM) and no cytotoxicity (CC ₅₀  > 100 μM). In extended biochemical assays compound 11d did not inhibit RT polymerase (pol) while inhibiting integrase strand transfer (INST) with 53 fold lower potency (IC ₅₀  = 2.1 μM) than RNase H inhibition. Crystallographic and molecular modeling studies confirmed the RNase H active site binding mode.

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Organizational Affiliation: 
• Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.
Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA.
Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA.
Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA; Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and 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: 234.44 kDa 
• Atom Count: 18,190 
• Modeled Residue Count: 1,953 
• Deposited Residue Count: 1,972 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A, C	557	Human immunodeficiency virus type 1 BH10	Mutation(s): 1  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)
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, D	429	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZW2	G [auth A], VA [auth C]	6-benzyl-3-hydroxythieno[2,3-d]pyrimidine-2,4(1H,3H)-dione C13 H10 N2 O3 S BATRIMGMBZXTOT-UHFFFAOYSA-N
PGE	H [auth A], TB [auth D], UB [auth D], W [auth B], X [auth B], Y [auth B], Z [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	AA [auth B], AB [auth C], AC [auth D], BA [auth B], BB [auth C], BC [auth D], CA [auth B], CB [auth C], CC [auth D], DA [auth B], DB [auth C], DC [auth D], EA [auth B], EB [auth C], EC [auth D], FA [auth B], FB [auth C], FC [auth D], GA [auth B], GB [auth C], GC [auth D], HA [auth B], HB [auth C], I [auth A], IA [auth B], IB [auth C], J [auth A], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], LB [auth C], M [auth A], MA [auth B], MB [auth C], N [auth A], NA [auth B], NB [auth C], O [auth A], OA [auth B], OB [auth C], P [auth A], PA [auth B], PB [auth C], Q [auth A], QA [auth B], QB [auth C], R [auth A], RA [auth B], RB [auth C], S [auth A], SA [auth B], SB [auth C], T [auth A], U [auth A], V [auth A], VB [auth D], WA [auth C], WB [auth D], XA [auth C], XB [auth D], YA [auth C], YB [auth D], ZA [auth C], ZB [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	E [auth A], F [auth A], TA [auth C], UA [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZW2	BindingDB:  6AOC	IC50: min: 43, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.37	α = 105.72
b = 89.12	β = 95.03
c = 112.73	γ = 110.72

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
MrBUMP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Kirby, K.A., Sarafianos, S.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI100890

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description