Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.43 kDa 
• Atom Count: 1747 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

6OXP

HIV-1 Protease NL4-3 WT in Complex with UMass3

• PDB DOI: 10.2210/pdb6OXP/pdb

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


• Deposited: 2019-05-14 Released: 2019-08-21 
• Deposition Author(s): Lockbaum, G.J., Rusere, L.N., Lee, S.K., Henes, M., Kosovrasti, K., Spielvogel, E., Nalivaika, E.A., Swanstrom, R., KurtYilmaz, N., Schiffer, C.A., Ali, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.217 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands To Optimize Hydrogen Bonding in the Substrate Envelope.

Rusere, L.N., Lockbaum, G.J., Lee, S.K., Henes, M., Kosovrasti, K., Spielvogel, E., Nalivaika, E.A., Swanstrom, R., Yilmaz, N.K., Schiffer, C.A., Ali, A.

(2019) J Med Chem 62: 8062-8079

• PubMed: 31386368 
• DOI: 10.1021/acs.jmedchem.9b00838
• Primary Citation of Related Structures:  
  6OXO, 6OXP, 6OXQ, 6OXR, 6OXS, 6OXT, 6OXU, 6OXV, 6OXW, 6OXX, 6OXY, 6OXZ, 6OY0, 6OY1, 6OY2


• PubMed Abstract: 
  

A structure-guided design strategy was used to improve the resistance profile of HIV-1 protease inhibitors by optimizing hydrogen bonding and van der Waals interactions with the protease while staying within the substrate envelope. Stereoisomers of 4-(1-hydroxyethyl)benzene and 4-(1,2-dihydroxyethyl)benzene moieties were explored as P2' ligands providing pairs of diastereoisomers epimeric at P2', which exhibited distinct potency profiles depending on the configuration of the hydroxyl group and size of the P1' group. While compounds with the 4-(1-hydroxyethyl)benzene P2' moiety maintained excellent antiviral potency against a panel of multidrug-resistant HIV-1 strains, analogues with the polar 4-(1,2-dihydroxyethyl)benzene moiety were less potent, and only the ( R )-epimer incorporating a larger 2-ethylbutyl P1' group showed improved potency. Crystal structures of protease-inhibitor complexes revealed strong hydrogen bonding interactions of both ( R )- and ( S )-stereoisomers of the hydroxyethyl group with Asp30'. Notably, the ( R )-dihydroxyethyl group was involved in a unique pattern of direct hydrogen bonding interactions with the backbone amides of Asp29' and Asp30'. The SAR data and analysis of crystal structures provide insights for optimizing these promising HIV-1 protease inhibitors.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease NL4-3	B [auth A], A [auth B]	99	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: pol EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K2A (Subject of Investigation/LOI)	E [auth A]	(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-({[4-(hydroxymethyl)phenyl]sulfonyl}[(2S)-2-methylbutyl]amino)propyl]carbamate C29 H40 N2 O8 S ALWBGUNCNDFMFE-QKULBLGOSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
K2A	BindingDB:  6OXP	Ki: min: 5.00e-4, max: 0.08 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.217 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51	α = 90
b = 58.028	β = 90
c = 62.146	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-05-14 
• Released Date: 2019-08-21 
Deposition Author(s): Lockbaum, G.J., Rusere, L.N., Lee, S.K., Henes, M., Kosovrasti, K., Spielvogel, E., Nalivaika, E.A., Swanstrom, R., KurtYilmaz, N., Schiffer, C.A., Ali, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01-GM109767

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence