9G1T | pdb_00009g1t

Human LTC4 synthase in complex with compound 5

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

  • Deposited: 2024-07-10 Released: 2025-02-26 
  • Deposition Author(s): Srinivas, H.
  • Funding Organization(s): Not funded

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.243 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9G1T

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 18.41 kDa 
  • Atom Count: 1,152 
  • Modeled Residue Count: 143 
  • Deposited Residue Count: 157 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IH0
(Subject of Investigation/LOI)

Query on A1IH0



Download:Ideal Coordinates CCD File
D [auth A]1-(4-chloranyl-3-fluoranyl-phenyl)-9-[(~{E})-3-phenylprop-2-enoyl]-1,9-diazaspiro[5.5]undecan-2-one
C24 H24 Cl F N2 O2
QOKKDKNMZGDVHI-DHZHZOJOSA-N
PLM

Query on PLM



Download:Ideal Coordinates CCD File
B [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
PAM

Query on PAM



Download:Ideal Coordinates CCD File
C [auth A]PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.243 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.352α = 90
b = 170.352β = 90
c = 170.352γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Not fundedSwitzerland--

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