3BC4 | pdb_00003bc4

I84V HIV-1 protease in complex with a pyrrolidine diester

• PDB DOI: https://doi.org/10.2210/pdb3BC4/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-12 Released: 2008-09-02 
• Deposition Author(s): Boettcher, J., Blum, A., Heine, A., Diederich, W.E., Klebe, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.241 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors

Blum, A., Heine, A., Diederich, W.E., Klebe, G.

(2008) ChemMedChem 3: 1337-1344

• PubMed: 18720485 
• DOI: https://doi.org/10.1002/cmdc.200800113
• Primary Citation Related Structures: 
  3BC4


• PubMed Abstract: 
  

  HIV protease is a well-established drug target in antiviral chemotherapy. Immense research efforts have been made to discover effective inhibitors, thus making the enzyme one of the most studied and best characterized proteins. Although the protease exhibits high flexibility, all approved drugs target virtually the same protein conformation. The development of viral cross-resistance demands the generation of inhibitors with novel scaffolds and deviating modes of binding. Herein we report the design and the short, high-yielding stereoselective synthesis of a series of chiral, symmetric pyrrolidine-based inhibitors targeting the open-flap conformation of the protease. The obtained co-crystal structure with one derivative provides a valuable starting point for further inhibitor design.

---

Organizational Affiliation: 
• Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

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: 11.33 kDa 
• Atom Count: 864 
• Modeled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protease	A	99	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5)) Explore P04587  Go to UniProtKB:  P04587

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LLG	B [auth A], C [auth A]	2-aminoethyl naphthalen-1-ylacetate C14 H15 N O2 PDCSQCHNOPNJMK-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.241 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.299	α = 90
b = 46.299	β = 90
c = 101.404	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Boettcher, J., Blum, A., Heine, A., Diederich, W.E., Klebe, G.

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2022-04-13
  Changes: Source and taxonomy
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description