3QRM | pdb_00003qrm

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

• PDB DOI: https://doi.org/10.2210/pdb3QRM/pdb

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


• Deposited: 2011-02-18 Released: 2012-02-22 
• Deposition Author(s): Lindemann, I., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.200 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

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: 22.47 kDa 
• Atom Count: 1,871 
• 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, 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
NK7	C [auth A]	4-{[4-(trifluoromethyl)benzyl][(3S,4S)-4-{[4-(trifluoromethyl)benzyl]amino}pyrrolidin-3-yl]sulfamoyl}benzamide C27 H26 F6 N4 O3 S UMJXENCLPLBDKV-ZEQRLZLVSA-N
DTD	E [auth A]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N
CL	D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.200 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.94	α = 90
b = 86.03	β = 90
c = 46.5	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: 2012-02-22 
Deposition Author(s): Lindemann, I., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description