5AH8 | pdb_00005ah8

Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease Inhibitors (II)

• PDB DOI: https://doi.org/10.2210/pdb5AH8/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2015-02-05 Released: 2015-05-06 
• Deposition Author(s): Hohlfeld, K., Wegner, J.K., Kesteleyn, B., Linclau, B., Unge, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: other

Literature

Disubstituted Bis-Thf Moieties as New P2 Ligands in Non-Peptidal HIV-1 Protease Inhibitors (II).

Hohlfeld, K., Wegner, J., Kesteleyn, B., Linclau, B., Unge, J.

(2015) J Med Chem 58: 4029

• PubMed: 25897791 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00358
• Primary Citation Related Structures: 
  5AGZ, 5AH6, 5AH7, 5AH8, 5AH9, 5AHA, 5AHB, 5AHC


• PubMed Abstract: 
  

  A series of darunavir analogues featuring a substituted bis-THF ring as P2 ligand have been synthesized and evaluated. Very high affinity protease inhibitors (PIs) with an interesting activity on wild-type HIV and a panel of multi-PI resistant HIV-1 mutants containing clinically observed, primary mutations were identified using a cell-based assay. Crystal structure analysis was conducted on a number of PI analogues in complex with HIV-1 protease.

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Organizational Affiliation: 
• †University of Southampton, School of Chemistry, Highfield, Southampton SO17 1BJ, United Kingdom.
‡Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium.
§Lund University, MAX-lab, Ole Römers väg 1, SE-223 63 Lund, 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: 22.37 kDa 
• Atom Count: 1,895 
• 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 (Z2/CDC-Z34 ISOLATE)	Mutation(s): 3  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
C7W	D [auth A]	(3R,3aS,4R,6aR)-4-(3,3,3-trifluoropropoxy)hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-3-hydroxy-4-[{[2-(methylamino)-1,3-benzoxazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-phenylbutan-2-yl}carbamate C32 H41 F3 N4 O9 S GBXWBYHBRMGXSH-DYJLPOQOSA-N
CL	C [auth A], E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.45	α = 90
b = 85.72	β = 90
c = 46.35	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Hohlfeld, K., Wegner, J.K., Kesteleyn, B., Linclau, B., Unge, J.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2015-05-27
  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