9Q13 | pdb_00009q13

Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor NR05-04

• PDB DOI: https://doi.org/10.2210/pdb9Q13/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-08-13 Released: 2025-12-24 
• Deposition Author(s): Kaur, J., Shaqra, A.M., Schiffer, C.A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Fluorinated HIV-1 Protease Inhibitors Containing Chiral Hydroxyethylbenzene and Indanol as P2' Ligands with Potent Activity Against Drug-Resistant Variants

Kaur, J., Spielvogel, E., Rao, D.N., Rusere, L.N., Shaqra, A.M., Lockbaum, G.J., Maryam, A., Yilmaz, N.K., Swanstrom, R., Schiffer, C.A., Ali, A.

(2026) Eur J Med Chem 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.48 kDa 
• Atom Count: 1,712 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A [auth B], B [auth A]	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CNJ (Subject of Investigation/LOI)	C [auth B]	(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-{[(1R)-1-hydroxy-2,3-dihydro-1H-indene-5-sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate C30 H38 F2 N2 O8 S ONIZIZRIOJVEAP-OUDUKYORSA-N
SO4	D [auth B], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.363	α = 90
b = 62.363	β = 90
c = 82.305	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Kaur, J., Shaqra, A.M., Schiffer, C.A.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release