9Q3P | pdb_00009q3p

Crystal Structure of WT HIV-1 Protease (NL4-3) with Inhibitor LR4-45

PDB DOI: https://doi.org/10.2210/pdb9Q3P/pdb

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

Deposited: 2025-08-19 Released: 2025-12-24
Deposition Author(s): Shaqra, A.M., Kaur, J., Schiffer, C.A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.242 (Depositor), 0.237 (DCC)
R-Value Work:
0.213 (Depositor), 0.208 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

To be published.

Macromolecule Content

Total Structure Weight: 22.37 kDa
Atom Count: 1,685
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CNY (Subject of Investigation/LOI) Query on A1CNY Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-({4-[(1S)-1-hydroxyethyl]benzene-1-sulfonyl}[(2S)-2-methylbutyl]amino)butan-2-yl]carbamate C₃₀ H₄₀ F₂ N₂ O₈ S TWPFEZUGJPMUHE-MPGHVIBCSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.242 (Depositor), 0.237 (DCC)
R-Value Work: 0.213 (Depositor), 0.208 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.433	α = 90
b = 62.433	β = 90
c = 82.016	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.