4ZLS

HIV-1 wild Type protease with GRL-096-13A (a Boc-derivative P2-Ligand, 3,-5-dimethylbiphenyl P1-Ligand)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Design of Potent HIV-1 Protease Inhibitors with Modified P1-Biphenyl Ligands: Synthesis, Biological Evaluation, and Enzyme-Inhibitor X-ray Structural Studies.

Ghosh, A.K.Yu, X.Osswald, H.L.Agniswamy, J.Wang, Y.F.Amano, M.Weber, I.T.Mitsuya, H.

(2015) J Med Chem 58: 5334-5343

  • DOI: 10.1021/acs.jmedchem.5b00676
  • Primary Citation of Related Structures:  
    4ZLS

  • PubMed Abstract: 
  • We report the design, synthesis, X-ray structural studies, and biological evaluation of a novel series of HIV-1 protease inhibitors. We designed a variety of functionalized biphenyl derivatives to make enhanced van der Waals interactions in the S1 subsite of HIV-1 protease ...

    We report the design, synthesis, X-ray structural studies, and biological evaluation of a novel series of HIV-1 protease inhibitors. We designed a variety of functionalized biphenyl derivatives to make enhanced van der Waals interactions in the S1 subsite of HIV-1 protease. These biphenyl derivatives were conveniently synthesized using a Suzuki-Miyaura cross-coupling reaction as the key step. We examined the potential of these functionalized biphenyl-derived P1 ligands in combination with 3-(S)-tetrahydrofuranyl urethane and bis-tetrahydrofuranyl urethane as the P2 ligands. Inhibitor 21e, with a 2-methoxy-1,1'-biphenyl derivative as P1 ligand and bis-THF as the P2 ligand, displayed the most potent enzyme inhibitory and antiviral activity. This inhibitor also exhibited potent activity against a panel of multidrug-resistant HIV-1 variants. A high resolution X-ray crystal structure of related Boc-derivative 17a-bound HIV-1 protease provided important molecular insight into the ligand-binding site interactions of the biphenyl core in the S1 subsite of HIV-1 protease.


    Organizational Affiliation

    ⊥Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseA, B99Human immunodeficiency virus type 1 BH10Mutation(s): 5 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 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 P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G61 (Subject of Investigation/LOI)
Query on G61

Download Ideal Coordinates CCD File 
F [auth B]tert-butyl [(2S,3R)-1-(3',5'-dimethoxybiphenyl-3-yl)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate
C34 H46 N2 O8 S
AHYAGCXJMLLYGM-AJQTZOPKSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], G [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
G61 Binding MOAD:  4ZLS Ki: 0.82 (nM) from 1 assay(s)
BindingDB:  4ZLS Ki: 0.82 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.74α = 90
b = 86.238β = 90
c = 46.067γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy