6R7D

Crystal structure of LTC4S in complex with AZ13690257


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of the Oral Leukotriene C4 Synthase Inhibitor (1S,2S)-2-({5-[(5-Chloro-2,4-difluorophenyl)(2-fluoro-2-methylpropyl)amino]-3-methoxypyrazin-2-yl}carbonyl)cyclopropanecarboxylic Acid (AZD9898) as a New Treatment for Asthma.

Munck Af Rosenschold, M.Johannesson, P.Nikitidis, A.Tyrchan, C.Chang, H.F.Ronn, R.Chapman, D.Ullah, V.Nikitidis, G.Glader, P.Kack, H.Bonn, B.Wagberg, F.Bjorkstrand, E.Andersson, U.Swedin, L.Rohman, M.Andreasson, T.Bergstrom, E.L.Jiang, F.Zhou, X.H.Lundqvist, A.J.Malmberg, A.Ek, M.Gordon, E.Pettersen, A.Ripa, L.Davis, A.M.

(2019) J Med Chem 62: 7769-7787

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00555
  • Primary Citation of Related Structures:  
    6R7D

  • PubMed Abstract: 

    While bronchodilators and inhaled corticosteroids are the mainstay of asthma treatment, up to 50% of asthmatics remain uncontrolled. Many studies show that the cysteinyl leukotriene cascade remains highly activated in some asthmatics, even those on high-dose inhaled or oral corticosteroids. Hence, inhibition of the leukotriene C4 synthase (LTC4S) enzyme could provide a new and differentiated core treatment for patients with a highly activated cysteinyl leukotriene cascade. Starting from a screening hit ( 3 ), a program to discover oral inhibitors of LTC4S led to (1 S ,2 S )-2-({5-[(5-chloro-2,4-difluorophenyl)(2-fluoro-2-methylpropyl)amino]-3-methoxypyrazin-2-yl}carbonyl)cyclopropanecarboxylic acid (AZD9898) ( 36 ), a picomolar LTC4S inhibitor (IC 50 = 0.28 nM) with high lipophilic ligand efficiency (LLE = 8.5), which displays nanomolar potency in cells (peripheral blood mononuclear cell, IC 50,free = 6.2 nM) and good in vivo pharmacodynamics in a calcium ionophore-stimulated rat model after oral dosing (in vivo, IC 50,free = 34 nM). Compound 36 mitigates the GABA binding, hepatic toxicity signal, and in vivo toxicology findings of an early lead compound 7 with a human dose predicted to be 30 mg once daily.


  • Organizational Affiliation

    Orexo AB , Virdings allé 32A , SE-75450 Uppsala , Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leukotriene C4 synthase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
157Homo sapiensMutation(s): 0 
Gene Names: LTC4S
EC: 4.4.1.20
Membrane Entity: Yes 
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

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

Download Ideal Coordinates CCD File 
CA [auth C]
DB [auth H]
GB [auth I]
JA [auth D]
KB [auth J]
CA [auth C],
DB [auth H],
GB [auth I],
JA [auth D],
KB [auth J],
M [auth A],
PA [auth E],
RB [auth K],
SB [auth L],
T [auth B],
TA [auth F],
YA [auth G]
(1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid
C24 H23 N3 O4
QYPOYXFLLPVCEL-ROUUACIJSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth G]
BB [auth G]
CB [auth G]
EA [auth C]
AA [auth B],
AB [auth G],
BB [auth G],
CB [auth G],
EA [auth C],
EB [auth H],
FA [auth C],
FB [auth H],
GA [auth C],
HA [auth C],
IA [auth C],
IB [auth I],
JB [auth I],
LA [auth D],
MA [auth D],
MB [auth J],
NA [auth D],
NB [auth J],
O [auth A],
OA [auth D],
OB [auth J],
P [auth A],
PB [auth J],
Q [auth A],
QA [auth E],
QB [auth J],
R [auth A],
RA [auth E],
S [auth A],
SA [auth E],
UA [auth F],
UB [auth L],
V [auth B],
VA [auth F],
VB [auth L],
W [auth B],
WA [auth F],
WB [auth L],
X [auth B],
XA [auth F],
XB [auth L],
Y [auth B],
Z [auth B]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
DA [auth C]
HB [auth I]
KA [auth D]
LB [auth J]
N [auth A]
DA [auth C],
HB [auth I],
KA [auth D],
LB [auth J],
N [auth A],
TB [auth L],
U [auth B],
ZA [auth G]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JUQ BindingDB:  6R7D IC50: 50 (nM) from 1 assay(s)
Binding MOAD:  6R7D IC50: 2.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.591α = 90
b = 169.385β = 90
c = 174.478γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-13
    Changes: Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description