9Y6C | pdb_00009y6c

X-ray structure analysis of human Complement Component 5 TE domain in complex with the peptide Ra30303

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.253 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of Zilucoplan: A Complement C5 Inhibitor for Treatment of Anti-Acetylcholine Receptor (AChR) Antibody-Positive Generalized Myasthenia Gravis (gMG).

Ye, P., Hammer, R.P., Wang, Z., Dhamnaskar, K., Hoarty, M., Ma, Z., Tang, G.Q., DeMarco, S.J., Ricardo, A.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02537
  • Primary Citation of Related Structures:  
    9Y6C

  • PubMed Abstract: 

    Complement component 5 (C5) is a protein in the complement cascade and a part of the innate immune system that has been clinically validated as a therapeutic target for several immune-mediated diseases including generalized myasthenia gravis (gMG). In this paper, we discuss the early discovery of zilucoplan, a macrocyclic peptide drug, which was identified via innovative extreme diversity mRNA display (Ma, Z.; Hartman, M. C. T. In Vitro Selection of Unnatural Cyclic Peptide Libraries via mRNA Display. In Ribosome Display and Related Technologies: Methods and Protocols ; Douthwaite, J. A., Jackson, R. H., Eds.; Springer: New York, 2012; pp 367-390.) against C5 and approved for the treatment of gMG. We highlight the key steps and rationale behind the peptide medicinal chemistry optimization of the initial screening hits, that led to improved potency, stability, and pharmacokinetic properties.

    • Organizational Affiliation: 
    • UCB Bioscience, Cambridge, Massachusetts 02140, United States.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C5324Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
Go to UniProtKB:  P01031
PHAROS:  P01031
GTEx:  ENSG00000106804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01031
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide Ra3030317synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
A1CTT
Query on A1CTT
B
D-PEPTIDE LINKINGC9 H11 N O2ALA
NVA
Query on NVA
B
L-PEPTIDE LINKINGC5 H11 N O2VAL
TBG
Query on TBG
B
L-PEPTIDE LINKINGC6 H13 N O2VAL
TRN
Query on TRN
B
L-PEPTIDE LINKINGC10 H11 N3 O2TRP
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.253 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.051α = 90
b = 112.025β = 90
c = 164.968γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release