3ZPS | pdb_00003zps

Design and Synthesis of P1-P3 Macrocyclic Tertiary Alcohol Comprising HIV-1 Protease Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3ZPS/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-03-01 Released: 2013-11-06 
• Deposition Author(s): Joshi, A., Veron, J.B., Unge, J., Rosenquist, A., Wallberg, H., Samuelsson, B., Hallberg, A., Larhed, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: other

Literature

Design and Synthesis of P1-P3 Macrocyclic Tertiary Alcohol Comprising HIV-1 Protease Inhibitors.

Joshi, A., Veron, J.B., Unge, J., Rosenquist, A., Wallberg, H., Samuelsson, B., Hallberg, A., Larhed, M.

(2013) J Med Chem 56: 8999

• PubMed: 24160253 
• DOI: https://doi.org/10.1021/jm400811d
• Primary Citation of Related Structures:  
  3ZPS, 3ZPT, 3ZPU


• PubMed Abstract: 
  

  To study P1-P3 macrocyclizations of previously reported tertiary-alcohol-comprising HIV-1 protease inhibitors (PIs), three new 14- and 15-member macrocyclic PIs were designed, synthesized by ring-closing metathesis, and evaluated alongside with 10 novel linear PIs. Cocrystallized complexes of the macrocyclic PIs and the HIV-1 protease are presented, analyzed, and discussed. The macrocyclic structures exhibited higher activities than the linear precursors with Ki and EC50 values down to 3.1 nM and 0.37 μM, respectively.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University , P.O. 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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.39 kDa 
• Atom Count: 1,851 
• 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 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EQM	F [auth B]	methyl N-[(2S)-1-[2-[(4-bromophenyl)methyl]-2-[(4R)-5-[[(2S)-3,3-dimethyl-1-oxidanylidene-1-(prop-2-enylamino)butan-2-yl]amino]-4-oxidanyl-5-oxidanylidene-4-(phenylmethyl)pentyl]hydrazinyl]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate C36 H52 Br N5 O6 SCBLWEFHRVDOAJ-DFNFTQNPSA-N
CL	C [auth A], D [auth B], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.84	α = 90
b = 85.94	β = 90
c = 46.28	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: 2013-11-06 
Deposition Author(s): Joshi, A., Veron, J.B., Unge, J., Rosenquist, A., Wallberg, H., Samuelsson, B., Hallberg, A., Larhed, M.

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2013-12-11
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description