6VCE

HIV-1 wild type protease with GRL-026-18A, a crown-like tetrahydropyranotetrahydrofuran with a bridged methylene group as a P2 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation 3D Report Full Report



Literature

Design, Synthesis, and X-ray Studies of Potent HIV-1 Protease Inhibitors with P2-Carboxamide Functionalities

Ghosh, A.K.Grillo, A.Raghavaiah, J.Kovela, S.Johnson, M.E.Kneller, D.W.Wang, Y.-F.Hattori, S.Higashi-Kuwata, N.Weber, I.T.Mitsuya, H.

(2020) ACS Med Chem Lett 


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ProteaseA, B99Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
Find proteins for Q5RZ08 (Human immunodeficiency virus 1)
Explore Q5RZ08 
Go to UniProtKB:  Q5RZ08
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6R
Query on G6R

Download CCD File 
B
N-[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]-2-[(3S,3aR,5S,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl]acetamide
C34 H42 F2 N4 O6 S2
BDFWTUGFCVLPRW-KVUOCWAWSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.904α = 90
b = 86.207β = 90
c = 46.09γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesAI150466
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAI150461
Japan Agency for Medical Research and Development (AMED)JapanJP15fk0410001
Japan Agency for Medical Research and Development (AMED)JapanJP16fk0410101
Other governmentUnited States--
Other governmentJapan--
Other governmentJapan--
Other governmentJapan--

Revision History 

  • Version 1.0: 2020-07-01
    Type: Initial release