10KT | pdb_000010kt

Crystal structure of A2A adenosine receptor A2AR-bRIL in complex with Compound50


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.243 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 10KT

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Discovery of MK-1088 as a Potent A 2A /A 2B Adenosine Receptor Dual-Antagonist for Cancer Immunotherapy.

Zhang, Y.Hennessy, E.Larsen, M.A.Hao, J.Pan, J.Mansoor, U.F.Sather, A.Brill, Z.G.Rico, L.Swaminathan, U.Moreno, J.Vara, B.A.Ranganath, S.Palmieri, A.Ogunbodede, O.Barry, E.R.Hinton, M.C.Daublain, P.Gupta, P.Chatterjee, M.Rottey, S.Presland, J.Hill, A.D.Dewey, W.J.Schneider, S.E.Ciaccio, P.J.Otte, K.M.Rindgen, D.Tatosian, D.Turnbull, B.W.H.Silverman, S.M.Chobanian, H.Krishnamurthy, H.Pang, L.Wnek, R.Afshar, R.Crowley, S.Miller, A.O'Neil, J.Chrencik, J.Plummer, C.W.Ali, A.Cumming, J.DeMong, D.E.

(2026) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c03405
  • Primary Citation Related Structures: 
    10KT

  • PubMed Abstract: 

    Immune cells expressing the adenosine A 2A receptor (A 2A R) and A 2B receptor (A 2B R) present in an adenosine-rich tumor microenvironment have suppressed effector functions, such as proinflammatory cytokine release, antigen presentation, and others, making them inert to cancer cells. Simultaneous blockade of the downstream effects mediated by both receptor subtypes with a dual inhibitor has the potential to reverse adenosine-mediated suppression of tumor immune surveillance as either a single-agent treatment or in combination with other immunotherapy agents such as anti-PD-1/PD-L1 monoclonal antibodies. This publication describes the discovery and optimization of a novel series of potent and selective dual A 2A R/A 2B R antagonists, resulting in compound 46 ( MK-1088 ) being identified for progression to human clinical studies.


  • Organizational Affiliation
    • Discovery Chemistry, Merck & Co., Inc., 126 E Lincoln Avenue, Rahway, New Jersey 07065, United States.

Macromolecule Content 

  • Total Structure Weight: 57.26 kDa 
  • Atom Count: 3,640 
  • Modeled Residue Count: 390 
  • 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
UniProt & NIH Common Fund Data Resources
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
GTEx:  ENSG00000128271 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P29274
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1C5S(
Subject of Investigation/LOI)

Query on A1C5S



Download:Ideal Coordinates CCD File
C [auth A](4%{S})-2-[(3%{R},6%{S})-1-(1-ethyl-1%{H}-pyrazol-4-yl)-6-methylpiperidin-3-yl]-7-methoxy[1,2,4]triazolo[1,5-%{c}]quinazolin-5-amine
C21 H26 N8 O
MTTLXYSEKMZHFP-UONOGXRCSA-N
CLR

Query on CLR



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

Query on OLB



Download:Ideal Coordinates CCD File
V [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
DA [auth A]
S [auth A]
T [auth A]
U [auth A]
W [auth A]
DA [auth A],
S [auth A],
T [auth A],
U [auth A],
W [auth A],
X [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]
EA [auth A]
FA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
EA [auth A],
FA [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]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PEG

Query on PEG



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

Query on NA



Download:Ideal Coordinates CCD File
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.243 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.37α = 90
b = 179.38β = 90
c = 140.55γ = 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
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-20
    Type: Initial release