XFEL crystal structure of the human cysteinyl leukotriene receptor 1 in complex with zafirlukast

Experimental Data Snapshot

  • Resolution: 2.53 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 3.3 of the entry. See complete history


Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs.

Luginina, A.Gusach, A.Marin, E.Mishin, A.Brouillette, R.Popov, P.Shiriaeva, A.Besserer-Offroy, E.Longpre, J.M.Lyapina, E.Ishchenko, A.Patel, N.Polovinkin, V.Safronova, N.Bogorodskiy, A.Edelweiss, E.Hu, H.Weierstall, U.Liu, W.Batyuk, A.Gordeliy, V.Han, G.W.Sarret, P.Katritch, V.Borshchevskiy, V.Cherezov, V.

(2019) Sci Adv 5: eaax2518-eaax2518

  • DOI: https://doi.org/10.1126/sciadv.aax2518
  • Primary Citation of Related Structures:  
    6RZ4, 6RZ5

  • PubMed Abstract: 

    The G protein-coupled cysteinyl leukotriene receptor CysLT 1 R mediates inflammatory processes and plays a major role in numerous disorders, including asthma, allergic rhinitis, cardiovascular disease, and cancer. Selective CysLT 1 R antagonists are widely prescribed as antiasthmatic drugs; however, these drugs demonstrate low effectiveness in some patients and exhibit a variety of side effects. To gain deeper understanding into the functional mechanisms of CysLTRs, we determined the crystal structures of CysLT 1 R bound to two chemically distinct antagonists, zafirlukast and pranlukast. The structures reveal unique ligand-binding modes and signaling mechanisms, including lateral ligand access to the orthosteric pocket between transmembrane helices TM4 and TM5, an atypical pattern of microswitches, and a distinct four-residue-coordinated sodium site. These results provide important insights and structural templates for rational discovery of safer and more effective drugs.

  • Organizational Affiliation

    Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1
A, B
423Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: CYSLTR1CYSLT1cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q9Y271 (Homo sapiens)
Explore Q9Y271 
Go to UniProtKB:  Q9Y271
GTEx:  ENSG00000173198 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7Q9Y271
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZLK (Subject of Investigation/LOI)
Query on ZLK

Download Ideal Coordinates CCD File 
C [auth A],
QA [auth B],
Y [auth B]
C31 H33 N3 O6 S
Query on OLC

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
DA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
J [auth A],
K [auth A],
Z [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
Query on OLA

Download Ideal Coordinates CCD File 
IA [auth B]
JA [auth B]
KA [auth B]
L [auth A]
LA [auth B]
IA [auth B],
JA [auth B],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
C18 H34 O2
Query on 1PE

Download Ideal Coordinates CCD File 
C10 H22 O6
Query on NA

Download Ideal Coordinates CCD File 
RA [auth B],
X [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
ZLK BindingDB:  6RZ5 Ki: min: 0.26, max: 2.3 (nM) from 6 assay(s)
IC50: min: 0.44, max: 44 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.53 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.11577/1660939
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.59α = 76.31
b = 68.58β = 76.68
c = 87.39γ = 81.21
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation16-14-10273
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127086
Canadian Institutes of Health ResearchCanadaFDN-148413

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 2.0: 2020-01-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 3.0: 2020-04-08
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.1: 2022-03-30
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 3.2: 2023-12-13
    Changes: Data collection, Database references
  • Version 3.3: 2024-01-24
    Changes: Refinement description