6DV0

HIV-1 wild type protease with GRL-02815A, a thiochroman heterocycle with (S)-Boc-amine functionality as the P2 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands.

Ghosh, A.K.Jadhav, R.D.Simpson, H.Kovela, S.Osswald, H.Agniswamy, J.Wang, Y.F.Hattori, S.I.Weber, I.T.Mitsuya, H.

(2018) Eur J Med Chem 160: 171-182


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
Find proteins for Q5RZ08 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q5RZ08
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GA8
Query on GA8

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B
tert-butyl [(4S)-6-{[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamoyl}-3,4-dihydro-2H-1-benzothiopyran-4-yl]carbamate
C36 H47 N3 O7 S2
FTKDNKJAEGHLKX-OWHBQTKESA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.719α = 90.00
b = 86.109β = 90.00
c = 46.193γ = 90.00
Software Package:
Software NamePurpose
SHELXLrefinement
PHASERphasing
HKL-2000data scaling
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
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: 2018-10-31
    Type: Initial release