6RZ5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 
    0.223 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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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 ZLKClick on this verticalbar to view details

This is version 3.4 of the entry. See complete history


Literature

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.


Macromolecules
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
PHAROS:  Q9Y271
GTEx:  ENSG00000173198 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7Q9Y271
Sequence Annotations
Expand
  • 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]
zafirlukast
C31 H33 N3 O6 S
YEEZWCHGZNKEEK-UHFFFAOYSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
DA [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
IA [auth B]
JA [auth B]
KA [auth B]
L [auth A]
LA [auth B]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
W [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
RA [auth B],
X [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ZLK BindingDB:  6RZ5 Ki: min: 0.26, max: 2.3 (nM) from 6 assay(s)
IC50: min: 0.26, max: 44 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free:  0.223 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.59α = 76.31
b = 68.58β = 76.68
c = 87.39γ = 81.21
Software Package:
Software NamePurpose
BUSTERrefinement
CrystFELdata reduction
CrystFELdata scaling
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 ZLKClick on this verticalbar to view details

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
  • Version 3.4: 2024-11-13
    Changes: Structure summary