2UY0

Two-Carbon-Elongated HIV-1 Protease Inhibitors with a Tertiary- Alcohol-Containing Transition-State Mimic

• PDB DOI: https://doi.org/10.2210/pdb2UY0/pdb

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


• Deposited: 2007-04-02 Released: 2008-05-20 
• Deposition Author(s): Ginman, N., Samuelsson, B., Hallberg, A., Unge, J.T., Unge, T.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.220 
• R-Value Work: 0.217 

Literature

Two-Carbon-Elongated HIV-1 Protease Inhibitors with a Tertiary-Alcohol-Containing Transition-State Mimic.

Wu, X., Ohrngren, P., Ekegren, J.K., Unge, J.T., Unge, T.K., Wallberg, H., Samuelsson, B., Hallberg, A., Larhed, M.

(2008) J Med Chem 51: 1053

• PubMed: 18215014 
• DOI: https://doi.org/10.1021/jm070680h
• Primary Citation of Related Structures:  
  2UXZ, 2UY0


• PubMed Abstract: 
  

  A new generation of HIV-1 protease inhibitors encompassing a tertiary-alcohol-based transition-state mimic has been developed. By elongation of the core structure of recently reported inhibitors with two carbon atoms and by varying the P1' group of the compounds, efficient inhibitors were obtained with Ki down to 2.3 nM and EC50 down to 0.17 microM. Two inhibitor-enzyme X-ray structures are reported.

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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: 22.33 kDa 
• Atom Count: 1,714 
• Modelled 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 P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HV1	C [auth B]	METHYL [(1S)-1-({2-[(4R)-4-BENZYL-4-HYDROXY-5-{[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]AMINO}-5-OXOPENTANOYL]-2-(4-BROMOBENZYL)HYDRAZINO}CARBONYL)-2,2-DIMETHYLPROPYL]CARBAMATE C36 H43 Br N4 O7 FPXYCCHKLAQWFU-AYZRFRAKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HV1	BindingDB:  2UY0	Ki: 120 (nM) from 1 assay(s)
	PDBBind:  2UY0	Ki: 120 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.220 
• R-Value Work: 0.217 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.88	α = 90
b = 85.71	β = 90
c = 46.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-20 
Deposition Author(s): Ginman, N., Samuelsson, B., Hallberg, A., Unge, J.T., Unge, T.K.

Revision History  

• Version 1.0: 2008-05-20
  Type: Initial release
  
• Version 1.1: 2011-06-02
  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: 2024-05-08
  Changes: Data collection, Database references