3QPJ

HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3QPJ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 (BRU ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-02-14 Released: 2012-02-15 
• Deposition Author(s): Lindemann, I., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Design of a series of novel three-armed pyrrolidine-based inhibitors for HIV-1 protease

Lindemann, I., Klee, N., Heine, A., Diederich, W.E., Klebe, G.

To be published.

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)

Macromolecule Content

• Total Structure Weight: 22.42 kDa 
• Atom Count: 1,824 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus type 1 (BRU ISOLATE)	Mutation(s): 3  EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N4I	D [auth B]	4-({(3S,4S)-4-[(3-hydroxybenzyl)amino]pyrrolidin-3-yl}[4-(trifluoromethyl)benzyl]sulfamoyl)benzamide C26 H27 F3 N4 O4 S ZYWFLXMDPHUHGO-ZEQRLZLVSA-N
DTD	G [auth B]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N
CL	C [auth A], E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.9	α = 90
b = 85.98	β = 90
c = 46.19	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Lindemann, I., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description