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 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report



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

  • 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 ...

    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

    Departments of Chemistry and Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1AB423Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: CYSLTR1CYSLT1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
cysteinyl leukotriene receptor 1 (CysLT1) in complex with pranlukast
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q9Y271 (Homo sapiens)
Explore Q9Y271 
Go to UniProtKB:  Q9Y271
NIH Common Fund Data Resources
PHAROS  Q9Y271
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZLK
Query on ZLK

Download Ideal Coordinates CCD File 
A, B
zafirlukast
C31 H33 N3 O6 S
YEEZWCHGZNKEEK-UHFFFAOYSA-N
 Ligand Interaction
OLC
Query on OLC

Download Ideal Coordinates CCD File 
A, B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
OLA
Query on OLA

Download Ideal Coordinates CCD File 
A, B
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
A
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZLKIC50:  2   nM  BindingDB
ZLKIC50:  1.899999976158142   nM  BindingDB
ZLKIC50:  5   nM  BindingDB
ZLKKi:  0.3400000035762787   nM  BindingDB
ZLKKi:  0.25999999046325684   nM  BindingDB
ZLKIC50:  0.4399999976158142   nM  BindingDB
ZLKKi:  2   nM  BindingDB
ZLKIC50:  14   nM  BindingDB
ZLKIC50:  1.7999999523162842   nM  BindingDB
ZLKKi:  0.30000001192092896   nM  BindingDB
ZLKKi:  2.299999952316284   nM  BindingDB
ZLKKi:  2   nM  BindingDB
ZLKIC50:  44   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • 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



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation16-14-10273
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM127086
Canadian Institutes of Health ResearchCanadaFDN-148413

Revision History 

  • 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