6MU8

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-386150 in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.993 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry.

Lai, Y.T.Wang, T.O'Dell, S.Louder, M.K.Schon, A.Cheung, C.S.F.Chuang, G.Y.Druz, A.Lin, B.McKee, K.Peng, D.Yang, Y.Zhang, B.Herschhorn, A.Sodroski, J.Bailer, R.T.Doria-Rose, N.A.Mascola, J.R.Langley, D.R.Kwong, P.D.

(2019) Nat Commun 10: 47-47

  • DOI: 10.1038/s41467-018-07851-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Diverse entry inhibitors targeting the gp120 subunit of the HIV-1 envelope (Env) trimer have been developed including BMS-626529, also called temsavir, a prodrug version of which is currently in phase III clinical trials. Here we report the character ...

    Diverse entry inhibitors targeting the gp120 subunit of the HIV-1 envelope (Env) trimer have been developed including BMS-626529, also called temsavir, a prodrug version of which is currently in phase III clinical trials. Here we report the characterization of a panel of small-molecule inhibitors including BMS-818251, which we show to be >10-fold more potent than temsavir on a cross-clade panel of 208-HIV-1 strains, as well as the engineering of a crystal lattice to enable structure determination of the interaction between these inhibitors and the HIV-1 Env trimer at higher resolution. By altering crystallization lattice chaperones, we identify a lattice with both improved diffraction and robust co-crystallization of HIV-1 Env trimers from different clades complexed to entry inhibitors with a range of binding affinities. The improved diffraction reveals BMS-818251 to utilize functional groups that interact with gp120 residues from the conserved β20-β21 hairpin to improve potency.


    Organizational Affiliation

    Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA.,Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, Cambridge, MA, 02142, USA.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA. pdkwong@nih.gov.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.,Computer Assisted Drug Design, Bristol-Myers Squibb Research and Development, Wallingford, CT, 06492, USA.,Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
B
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
35O22 scFv heavy chain portion
D
134N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
35O22 scFv light chain portion
E
114N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
G
481Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
3H109L Fab heavy chain
H
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
3H109L Fab light chain
L
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
JYS
Query on JYS

Download SDF File 
Download CCD File 
G
1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-1,2-dione
C21 H17 Br F N3 O3
FHPUNKHJTFLQMK-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, D, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.993 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 131.410α = 90.00
b = 131.410β = 90.00
c = 315.470γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release