5UV5 | pdb_00005uv5

Crystal Structure of a 2-Hydroxyisoquinoline-1,3-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase

• PDB DOI: https://doi.org/10.2210/pdb5UV5/pdb

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


• Deposited: 2017-02-19 Released: 2017-08-16 
• 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.287 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase.

Kirby, K.A., Myshakina, N.A., Christen, M.T., Chen, Y.L., Schmidt, H.A., Huber, A.D., Xi, Z., Kim, S., Rao, R.K., Kramer, S.T., Yang, Q., Singh, K., Parniak, M.A., Wang, Z., Ishima, R., Sarafianos, S.G.

(2017) Antimicrob Agents Chemother 61

• PubMed: 28760905 
• DOI: https://doi.org/10.1128/AAC.01351-17
• Primary Citation Related Structures: 
  5UV5


• PubMed Abstract: 
  

  The RNase H (RNH) function of HIV-1 reverse transcriptase (RT) plays an essential part in the viral life cycle. We report the characterization of YLC2-155, a 2-hydroxyisoquinoline-1,3-dione (HID)-based active-site RNH inhibitor. YLC2-155 inhibits both polymerase (50% inhibitory concentration [IC ₅₀ ] = 2.6 μM) and RNH functions (IC ₅₀ = 0.65 μM) of RT but is more effective against RNH. X-ray crystallography, nuclear magnetic resonance (NMR) analysis, and molecular modeling were used to show that YLC2-155 binds at the RNH-active site in multiple conformations.

---

Organizational Affiliation: 
• Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA [e-mail] [e-mail].
Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA.
Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
Department of Natural Science, Chatham University, Pittsburgh, Pennsylvania, USA.
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota, USA.
Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA.
Department of Biological Engineering, University of Missouri, Columbia, Missouri, USA.
Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA.
Department of Biochemistry, University of Missouri, Columbia, Missouri, USA.

Biological Assembly 1  

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

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: 229.11 kDa 
• Atom Count: 15,370 
• Modeled Residue Count: 1,873 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y55	G [auth A], J [auth C]	7-(furan-2-yl)-2-hydroxyisoquinoline-1,3(2H,4H)-dione C13 H9 N O4 FMBJYDTZYGCAIN-UHFFFAOYSA-N
MN	E [auth A], F [auth A], H [auth C], I [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.287 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.99	α = 105.53
b = 88.67	β = 93.41
c = 108.86	γ = 110.13

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Kirby, K.A., Sarafianos, S.G.

---

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: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2017-10-04
  Changes: Database references
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description