8GMN | pdb_00008gmn

Crystal structure of human C1s in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.281 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Discovery of a Novel Series of Potent, Selective, Orally Available, and Brain-Penetrable C1s Inhibitors for Modulation of the Complement Pathway.

Ikeda, Z.Kamei, T.Sasaki, Y.Reynolds, M.Sakai, N.Yoshikawa, M.Tawada, M.Morishita, N.Dougan, D.R.Chen, C.H.Levin, I.Zou, H.Kuno, M.Arimura, N.Kikukawa, Y.Kondo, M.Tohyama, K.Sato, K.

(2023) J Med Chem 66: 6354-6371

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00348
  • Primary Citation Related Structures: 
    8GMN

  • PubMed Abstract: 

    A novel series of non-amidine-based C1s inhibitors have been explored. Starting from high-throughput screening hit 3 , isoquinoline was replaced with 1-aminophthalazine to enhance C1s inhibitory activity while exhibiting good selectivity against other serine proteases. We first disclose a crystal structure of a complex of C1s and a small-molecule inhibitor ( 4e ), which guided structure-based optimization around the S2 and S3 sites to further enhance C1s inhibitory activity by over 300-fold. Improvement of membrane permeability by incorporation of fluorine at the 8-position of 1-aminophthalazine led to identification of ( R )-8 as a potent, selective, orally available, and brain-penetrable C1s inhibitor. ( R )-8 significantly inhibited membrane attack complex formation induced by human serum in a dose-dependent manner in an in vitro assay system, proving that selective C1s inhibition blocked the classical complement pathway effectively. As a result, ( R )-8 emerged as a valuable tool compound for both in vitro and in vivo assessment.


  • Organizational Affiliation
    • Research, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.

Macromolecule Content 

  • Total Structure Weight: 164.67 kDa 
  • Atom Count: 8,721 
  • Modeled Residue Count: 1,077 
  • Deposited Residue Count: 1,484 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Complement C1s subcomponent
A, B, C, D
371Homo sapiensMutation(s): 0 
Gene Names: C1S
EC: 3.4.21.42
UniProt & NIH Common Fund Data Resources
Find proteins for P09871 (Homo sapiens)
Explore P09871 
Go to UniProtKB:  P09871
PHAROS:  P09871
GTEx:  ENSG00000182326 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09871
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.281 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.471α = 86.13
b = 77.647β = 79.09
c = 108.484γ = 71.08
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 2.0: 2023-05-24
    Changes: Advisory, Atomic model, Database references, Structure summary
  • Version 2.1: 2024-11-20
    Changes: Data collection, Structure summary