6RZ6

Crystal structure of the human cysteinyl leukotriene receptor 2 in complex with ONO-2570366 (C2221 space group)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis of ligand selectivity and disease mutations in cysteinyl leukotriene receptors.

Gusach, A.Luginina, A.Marin, E.Brouillette, R.L.Besserer-Offroy, E.Longpre, J.M.Ishchenko, A.Popov, P.Patel, N.Fujimoto, T.Maruyama, T.Stauch, B.Ergasheva, M.Romanovskaia, D.Stepko, A.Kovalev, K.Shevtsov, M.Gordeliy, V.Han, G.W.Katritch, V.Borshchevskiy, V.Sarret, P.Mishin, A.Cherezov, V.

(2019) Nat Commun 10: 5573-5573

  • DOI: https://doi.org/10.1038/s41467-019-13348-2
  • Primary Citation of Related Structures:  
    6RZ6, 6RZ7, 6RZ8, 6RZ9

  • PubMed Abstract: 

    Cysteinyl leukotriene G protein-coupled receptors CysLT 1 and CysLT 2 regulate pro-inflammatory responses associated with allergic disorders. While selective inhibition of CysLT 1 R has been used for treating asthma and associated diseases for over two decades, CysLT 2 R has recently started to emerge as a potential drug target against atopic asthma, brain injury and central nervous system disorders, as well as several types of cancer. Here, we describe four crystal structures of CysLT 2 R in complex with three dual CysLT 1 R/CysLT 2 R antagonists. The reported structures together with the results of comprehensive mutagenesis and computer modeling studies shed light on molecular determinants of CysLTR ligand selectivity and specific effects of disease-related single nucleotide variants.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteinyl leukotriene receptor 2,Soluble cytochrome b562,Cysteinyl leukotriene receptor 2405Homo sapiensEscherichia coliMutation(s): 6 
Gene Names: CYSLTR2CYSLT2CYSLT2RPSEC0146cybC
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for Q9NS75 (Homo sapiens)
Go to UniProtKB:  Q9NS75
PHAROS:  Q9NS75
GTEx:  ENSG00000152207 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KNW (Subject of Investigation/LOI)
Query on KNW

Download Ideal Coordinates CCD File 
B [auth A](2~{S})-8-[[4-[4-(2-chloranyl-5-fluoranyl-phenyl)butoxy]phenyl]carbonylamino]-4-(4-oxidanyl-4-oxidanylidene-butyl)-2,3- dihydro-1,4-benzoxazine-2-carboxylic acid
C30 H30 Cl F N2 O7
JCUVQOJHURMRKB-SANMLTNESA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
U [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
1PE
Query on 1PE

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

Download Ideal Coordinates CCD File 
D [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.81α = 90
b = 170.88β = 90
c = 85.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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 ResearchCanada--
Fonds de Recherche du Quebec - Nature et TechnologiesCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description