7KMH

LY-CoV488 neutralizing antibody against SARS-CoV-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates.

Jones, B.E.Brown-Augsburger, P.L.Corbett, K.S.Westendorf, K.Davies, J.Cujec, T.P.Wiethoff, C.M.Blackbourne, J.L.Heinz, B.A.Foster, D.Higgs, R.E.Balasubramaniam, D.Wang, L.Zhang, Y.Yang, E.S.Bidshahri, R.Kraft, L.Hwang, Y.Zentelis, S.Jepson, K.R.Goya, R.Smith, M.A.Collins, D.W.Hinshaw, S.J.Tycho, S.A.Pellacani, D.Xiang, P.Muthuraman, K.Sobhanifar, S.Piper, M.H.Triana, F.J.Hendle, J.Pustilnik, A.Adams, A.C.Berens, S.J.Baric, R.S.Martinez, D.R.Cross, R.W.Geisbert, T.W.Borisevich, V.Abiona, O.Belli, H.M.de Vries, M.Mohamed, A.Dittmann, M.Samanovic, M.I.Mulligan, M.J.Goldsmith, J.A.Hsieh, C.L.Johnson, N.V.Wrapp, D.McLellan, J.S.Barnhart, B.C.Graham, B.S.Mascola, J.R.Hansen, C.L.Falconer, E.

(2021) Sci Transl Med 13

  • DOI: https://doi.org/10.1126/scitranslmed.abf1906
  • Primary Citation of Related Structures:  
    7KMG, 7KMH, 7KMI

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) poses a public health threat for which preventive and therapeutic agents are urgently needed. Neutralizing antibodies are a key class of therapeutics that may bridge widespread vaccination campaigns and offer a treatment solution in populations less responsive to vaccination. Here, we report that high-throughput microfluidic screening of antigen-specific B cells led to the identification of LY-CoV555 (also known as bamlanivimab), a potent anti-spike neutralizing antibody from a hospitalized, convalescent patient with coronavirus disease 2019 (COVID-19). Biochemical, structural, and functional characterization of LY-CoV555 revealed high-affinity binding to the receptor-binding domain, angiotensin-converting enzyme 2 binding inhibition, and potent neutralizing activity. A pharmacokinetic study of LY-CoV555 conducted in cynomolgus monkeys demonstrated a mean half-life of 13 days and a clearance of 0.22 ml hour -1 kg -1 , consistent with a typical human therapeutic antibody. In a rhesus macaque challenge model, prophylactic doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract in samples collected through study day 6 after viral inoculation. This antibody has entered clinical testing and is being evaluated across a spectrum of COVID-19 indications, including prevention and treatment.


  • Organizational Affiliation

    Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA. jones_bryan_edward@lilly.com ester.falconer@abcellera.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LY-CoV488 Fab heavy chain219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LY-CoV488 Fab light chain212Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1205Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.806α = 90
b = 260.59β = 90
c = 94.997γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description