8C9W | pdb_00008c9w

Crystal structure of the adenosine A2A receptor (construct A2A-PSB2-bRIL) complexed with Etrumadenant at the orthosteric pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of adenosine A 2A receptor in complex with clinical candidate Etrumadenant reveals unprecedented antagonist interaction.

Claff, T.Schlegel, J.G.Voss, J.H.Vaassen, V.J.Weisse, R.H.Cheng, R.K.Y.Markovic-Mueller, S.Bucher, D.Strater, N.Muller, C.E.

(2023) Commun Chem 6: 106-106

  • DOI: https://doi.org/10.1038/s42004-023-00894-6
  • Primary Citation Related Structures: 
    8C9W, 8CIC

  • PubMed Abstract: 

    The G s  protein-coupled adenosine A 2A receptor (A 2A AR) represents an emerging drug target for cancer immunotherapy. The clinical candidate Etrumadenant was developed as an A 2A AR antagonist with ancillary blockade of the A 2B AR subtype. It constitutes a unique chemotype featuring a poly-substituted 2-amino-4-phenyl-6-triazolylpyrimidine core structure. Herein, we report two crystal structures of the A 2A AR in complex with Etrumadenant, obtained with differently thermostabilized A 2A AR constructs. This led to the discovery of an unprecedented interaction, a hydrogen bond of T88 3.36 with the cyano group of Etrumadenant. T88 3.36 is mutated in most A 2A AR constructs used for crystallization, which has prevented the discovery of its interactions. In-vitro characterization of Etrumadenant indicated low selectivity versus the A 1 AR subtype, which can be rationalized by the structural data. These results will facilitate the future design of AR antagonists with desired selectivity. Moreover, they highlight the advantages of the employed A 2A AR crystallization construct that is devoid of ligand binding site mutations.


  • Organizational Affiliation
    • PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113, Bonn, Germany. tobias.claff@uni-bonn.de.

Macromolecule Content 

  • Total Structure Weight: 52.33 kDa 
  • Atom Count: 3,374 
  • Modeled Residue Count: 387 
  • Deposited Residue Count: 431 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adenosine receptor A2a,Soluble cytochrome b562431Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: ADORA2AADORA2cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
GTEx:  ENSG00000128271 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P29274
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U30
(Subject of Investigation/LOI)

Query on U30



Download:Ideal Coordinates CCD File
B [auth A]3-[2-azanyl-6-[1-[[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]methyl]-1,2,3-triazol-4-yl]pyrimidin-4-yl]-2-methyl-benzenecarbonitrile
C23 H22 N8 O
BUXIAWLTBSXYSW-UHFFFAOYSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLB

Query on OLB



Download:Ideal Coordinates CCD File
K [auth A](2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
OLC

Query on OLC



Download:Ideal Coordinates CCD File
J [auth A],
L [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
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
M [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.155α = 90
b = 178.226β = 90
c = 139.595γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-11-06
    Changes: Structure summary