6RZ4

Crystal structure of cysteinyl leukotriene receptor 1 in complex with pranlukast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

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
  • Structures With Same Primary Citation

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteinyl leukotriene receptor 1,Soluble cytochrome b562,Cysteinyl leukotriene receptor 1A423Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: CYSLTR1CYSLT1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KNT
Query on KNT

Download CCD File 
A
pranlukast
C27 H23 N5 O4
NBQKINXMPLXUET-UHFFFAOYSA-N
 Ligand Interaction
OLC
Query on OLC

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

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KNTIC50:  4.300000190734863   nM  BindingDB
KNTKi:  0.800000011920929   nM  BindingDB
KNTIC50:  0.800000011920929   nM  BindingDB
KNTKi:  0.800000011920929   nM  BindingDB
KNTKd:  0   nM  BindingDB
KNTIC50:  1   nM  BindingDB
KNTIC50:  0.03999999910593033   nM  BindingDB
KNTIC50:  4.400000095367432   nM  BindingDB
KNTIC50:  23   nM  BindingDB
KNTIC50:  0.03999999910593033   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.63α = 90
b = 45.35β = 91.47
c = 86.43γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata 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, Database references, Derived calculations, Structure summary