2BQV | pdb_00002bqv

HIV-1 protease in complex with inhibitor AHA455

• PDB DOI: https://doi.org/10.2210/pdb2BQV/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-04-28 Released: 2005-12-14 
• Deposition Author(s): Unge, T., Ekegren, J.K., Schenk, H.V., Zreik Safa, M., Wallberg, H., Samuelsson, B., Hallberg, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

A New Class of HIV-1 Protease Inhibitors Containing a Tertiary Alcohol in the Transition-State Mimicking Scaffold.

Ekegren, J.K., Unge, T., Safa, M.Z., Wallberg, H., Samuelsson, B., Hallberg, A.

(2005) J Med Chem 48: 8098

• PubMed: 16335934 
• DOI: https://doi.org/10.1021/jm050790t
• Primary Citation Related Structures: 
  2BQV


• PubMed Abstract: 
  

  Novel HIV-1 protease inhibitors encompassing a tertiary alcohol as part of the transition-state mimicking unit have been synthesized. Variation of the P1'-P3' residues and alteration of the tertiary alcohol absolute stereochemistry afforded 10 inhibitors. High potencies for the compounds with (S)-configuration at the carbon carrying the tertiary hydroxyl group were achieved with Ki values down to 2.4 nM. X-ray crystallographic data for a representative compound in complex with HIV-1 protease are presented.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 22.2 kDa 
• Atom Count: 1,606 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  EC: 3.4.23.16
UniProt
Find proteins for O92139 (Human immunodeficiency virus type 1) Explore O92139  Go to UniProtKB:  O92139

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A	C [auth A]	6-AMINO HEXANOIC ACID C33 H40 N4 O6 KEFISYJDRSSULW-GQPDOWDHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.243 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.082	α = 90
b = 87.452	β = 90
c = 47.124	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-14 
Deposition Author(s): Unge, T., Ekegren, J.K., Schenk, H.V., Zreik Safa, M., Wallberg, H., Samuelsson, B., Hallberg, A.

Revision History  

• Version 1.0: 2005-12-14
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description