9G0U

Human LTC4 synthase in complex with AZD9898

  • Classification: LYASE
  • Organism(s): Homo sapiens
  • Expression System: Pichia
  • Mutation(s): No 

  • Deposited: 2024-07-08 Released: 2025-02-26 
  • Deposition Author(s): Srinivas, H.
  • Funding Organization(s): Other private

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.220 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IHJClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Discovery of GJG057, a Potent and Highly Selective Inhibitor of Leukotriene C4 Synthase.

Thoma, G.Miltz, W.Waelchli, R.Orain, D.Spanka, C.Decoret, O.Wolf, R.M.Hurley, B.Cheung, A.K.Sandham, D.A.Honda, A.Tichkule, R.Chen, X.Patel, T.Labbe-Giguere, N.Tan, K.L.Springer, C.Manchester, J.Culshaw, A.J.Hunt, P.Srinivas, H.Penno, C.A.Ferrand, S.Numao, S.Schopfer, U.Jager, P.Wack, N.Hasler, F.Urban, B.Sindelar, M.Loetscher, P.Kiffe, M.Ren, X.Nicklin, P.White, K.Subramanian, K.Liu, H.Growcott, E.J.Rohn, T.A.

(2025) J Med Chem 68: 4721-4742

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02897
  • Primary Citation of Related Structures:  
    9G0U, 9G0V, 9G14, 9G1T

  • PubMed Abstract: 

    Leukotriene C4 synthase (LTC4S) is a glutathione S -transferase that mediates the biosynthesis of cysteinyl leukotriene C4 (LTC4). Cysteinyl leukotrienes (CysLTs) are lipid mediators that drive type 2 inflammation, bronchoconstriction, and itch. Thus, LTC4S represents an attractive drug target for the treatment of allergic inflammatory diseases, but to date, no LTC4S inhibitor has been tested in patients. Herein, we disclose the discovery and preclinical profiling of the highly selective, oral LTC4S inhibitor GJG057 (compound 1 ), which exhibits 20-fold improved potency (IC 50 = 44 nM) versus clinical candidate AZD9898 (IC 50 = 900 nM) in a human whole blood LTC4 release assay. GJG057 showed efficacy in a murine asthma exacerbation model as well as in a mastoparan-induced skin challenge PK/PD model and was profiled in GLP toxicology studies. Despite its promising properties, GJG057 was not progressed into clinical trials as an oral drug. Its potential as a topical drug is currently being evaluated.


  • Organizational Affiliation

    Global Discovery Chemistry, Biomedical Research, Novartis Pharma AG, Basel 4002, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leukotriene C4 synthase157Homo sapiensMutation(s): 0 
Gene Names: LTC4S
EC: 4.4.1.20 (PDB Primary Data), 2.5.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16873 (Homo sapiens)
Explore Q16873 
Go to UniProtKB:  Q16873
PHAROS:  Q16873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16873
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
R [auth A]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
A1IHJ (Subject of Investigation/LOI)
Query on A1IHJ

Download Ideal Coordinates CCD File 
V [auth A](1~{S},2~{S})-2-[5-[[5-chloranyl-2,4-bis(fluoranyl)phenyl]-(2-fluoranyl-2-methyl-propyl)amino]-3-methoxy-pyrazin-2-yl]carbonylcyclopropane-1-carboxylic acid
C20 H19 Cl F3 N3 O4
RVMWIVNHZMXEHS-UWVGGRQHSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
C [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
PAM
Query on PAM

Download Ideal Coordinates CCD File 
D [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.220 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.59α = 90
b = 177.59β = 90
c = 177.59γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IHJClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2025-02-26 
  • Deposition Author(s): Srinivas, H.

Funding OrganizationLocationGrant Number
Other privateSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references