8VU9 | pdb_00008vu9

Crystal structure of wild-type HIV-1 reverse transcriptase in complex with non-nucleoside inhibitor 5i3

• PDB DOI: https://doi.org/10.2210/pdb8VU9/pdb

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


• Deposited: 2024-01-29 Released: 2025-05-07 
• Deposition Author(s): Rumrill, S., Ruiz, F.X., Arnold, E.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Diarylpyrimidine-evolved HIV-1 non-nucleoside reverse transcriptase inhibitors show improved resistance and pharmacokinetic profiles against highly drug-resistant strains

Wang, Z., Rumrill, S.R., Kang, D., Desta, S., Feng, D., De Clercq, E., Pannecouque, C., Chen, C.H., Arnold, E., Ruiz, F.X., Liu, X., Zhan, P.

To be published.

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: 115.45 kDa 
• Atom Count: 8,795 
• Modelled Residue Count: 970 
• Deposited Residue Count: 984 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A	556	Human immunodeficiency virus type 1 BH10	Mutation(s): 3  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

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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WB3 (Subject of Investigation/LOI)	C [auth A]	(2E)-3-[4-({2-[(1-{[4-(methanesulfonyl)phenyl]methyl}piperidin-4-yl)amino]pyrido[2,3-d]pyrimidin-4-yl}oxy)-3,5-dimethylphenyl]prop-2-enenitrile C31 H32 N6 O3 S GIPFCGYDMDLDIO-GQCTYLIASA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth A], I [auth A], M [auth B], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.039	α = 90
b = 72.424	β = 100.065
c = 109	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Rumrill, S., Ruiz, F.X., Arnold, E.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI027690
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM008339
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM135141

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release