9PYX | pdb_00009pyx

Crystal structure of WT HIV-1 protease (NL4-3) with inhibitor J02-30

PDB DOI: https://doi.org/10.2210/pdb9PYX/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.247 (Depositor), 0.242 (DCC)
R-Value Work:
0.193 (Depositor), 0.189 (DCC)
R-Value Observed:
0.196 (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., 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

Macromolecule Content

Total Structure Weight: 22.4 kDa
Atom Count: 1,750
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
A1CM5 (Subject of Investigation/LOI) Query on A1CM5 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)-4-[(2-ethylbutyl){4-[(1R)-1-hydroxyethyl]benzene-1-sulfonyl}amino]-3-hydroxybutan-2-yl}carbamate C₃₁ H₄₂ F₂ N₂ O₈ S QSTWKEAHGIUFAI-KKWHVFEBSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.247 (Depositor), 0.242 (DCC)
R-Value Work: 0.193 (Depositor), 0.189 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.346	α = 90
b = 62.346	β = 90
c = 82.033	γ = 120

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

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.