6E7J

HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one with a bicyclic oxazolidinone scaffold as the P2 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and Synthesis of Potent HIV-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold as the P2 Ligands: Structure-Activity Studies and Biological and X-ray Structural Studies.

Ghosh, A.K.Williams, J.N.Ho, R.Y.Simpson, H.M.Hattori, S.I.Hayashi, H.Agniswamy, J.Wang, Y.F.Weber, I.T.Mitsuya, H.

(2018) J. Med. Chem. 61: 9722-9737


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
Find proteins for Q5RZ08 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q5RZ08
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HWY
Query on HWY

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Download CCD File 
A
(3aS,5R,6aR)-2-oxo-3-phenylhexahydro-2H-cyclopenta[d][1,3]oxazol-5-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate
C34 H41 N3 O8 S
MCFYAJCOYWLLEO-YGMVDIOKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.793α = 90.00
b = 86.043β = 90.00
c = 45.875γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXLrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesGM53386
National Institutes of Health/National Cancer InstituteUnited StatesGM62920
National Institutes of Health/National Cancer InstituteUnited Statesthe Intramural Research Program of the Center for Cancer Research
Department of Energy (United States)United StatesW-31-109-Eng-38
National Institutes of Health/National Cancer InstituteUnited Statesthe Intramural Research Program of the Center for Cancer Research
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japana Grant-in-Aid for Scientific Research (Priority Areas)
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanthe Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo)

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references