4UIP

The complex structure of extracellular domain of EGFR with Repebody (rAC1).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Enzymatic Prenylation and Oxime Ligation for the Synthesis of Stable and Homogeneous Protein-Drug Conjugates for Targeted Therapy.

Lee, J.Choi, H.Yun, M.Kang, Y.Jung, J.Ryu, Y.Kim, T.Y.Cha, Y.Cho, H.Min, J.Chung, C.Kim, H.

(2015) Angew Chem Int Ed Engl 54: 12020

  • DOI: https://doi.org/10.1002/anie.201505964
  • Primary Citation of Related Structures:  
    4UIP

  • PubMed Abstract: 

    Targeted therapy based on protein-drug conjugates has attracted significant attention owing to its high efficacy and low side effects. However, efficient and stable drug conjugation to a protein binder remains a challenge. Herein, a chemoenzymatic method to generate highly stable and homogenous drug conjugates with high efficiency is presented. The approach comprises the insertion of the CaaX sequence at the C-terminal end of the protein binder, prenylation using farnesyltransferase, and drug conjugation through an oxime ligation reaction. MMAF and an EGFR-specific repebody are used as the antitumor agent and protein binder, respectively. The method enables the precisely controlled synthesis of repebody-drug conjugates with high yield and homogeneity. The utility of this approach is illustrated by the notable stability of the repebody-drug conjugates in human plasma, negligible off-target effects, and a remarkable antitumor activity in vivo. The present method can be widely used for generating highly homogeneous and stable PDCs for targeted therapy.


  • Organizational Affiliation

    Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon (Korea).


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EPIDERMAL GROWTH FACTOR RECEPTOR618Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
REPEBODY (RAC1)251Listeria monocytogenessynthetic constructEptatretus burgeri
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for Q4G1L3 (Eptatretus burgeri)
Explore Q4G1L3 
Go to UniProtKB:  Q4G1L3
Find proteins for E0ACT6 (Listeria monocytogenes)
Explore E0ACT6 
Go to UniProtKB:  E0ACT6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsE0ACT6Q4G1L3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.79α = 90
b = 88.34β = 90
c = 189.21γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Structure summary
  • Version 1.2: 2017-03-15
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary