7QVK

NM-02 in complex with HER2-ECD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.275 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Co-crystallisation and humanisation of an anti-HER2 single-domain antibody as a theranostic tool.

Sawmynaden, K.Wong, N.Davies, S.Cowan, R.Brown, R.Tang, D.Henry, M.Tickle, D.Matthews, D.Carr, M.Bakrania, P.Hoi Ting, H.Hall, G.

(2023) PLoS One 18: e0288259-e0288259

  • DOI: https://doi.org/10.1371/journal.pone.0288259
  • Primary Citation of Related Structures:  
    7QVK

  • PubMed Abstract: 

    Human epidermal growth factor receptor-2 (HER2) is a well-recognised biomarker associated with 25% of breast cancers. In most cases, early detection and/or treatment correlates with an increased chance of survival. This study, has identified and characterised a highly specific anti-HER2 single-domain antibody (sdAb), NM-02, as a potential theranostic tool. Complete structural description by X-ray crystallography has revealed a non-overlapping epitope with current anti-HER2 antibodies. To reduce the immunogenicity risk, NM-02 underwent a humanisation process and retained wild type-like binding properties. To further de-risk the progression towards chemistry, manufacturing and control (CMC) we performed full developability profiling revealing favourable thermal and physical biochemical 'drug-like' properties. Finally, the application of the lead humanised NM-02 candidate (variant K) for HER2-specific imaging purposes was demonstrated using breast cancer HER2+/BT474 xenograft mice.


  • Organizational Affiliation

    LifeArc, Open Innovation Campus, Stevenage, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-2A [auth AAA]630Homo sapiensMutation(s): 0 
Gene Names: ERBB2HER2MLN19NEUNGL
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens)
Explore P04626 
Go to UniProtKB:  P04626
PHAROS:  P04626
GTEx:  ENSG00000141736 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04626
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NM-02B [auth BBB]132Camelus bactrianusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth AbA]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth AAA]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.275 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.767α = 90
b = 105.767β = 90
c = 185.882γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description