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Entry
Database: EMDB / ID: EMD-63614
TitleStructure-based discovery of potent agonists of the orphan receptor GPR139
Map data
Sample
  • Complex: GPR139_Gs/q
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nanobody 35
    • Protein or peptide: Endo-1,4-beta-xylanase,Probable G-protein coupled receptor 139
  • Ligand: 2-[5-(4-methylthiophen-3-yl)-1,2,4-oxadiazol-3-yl]-~{N}-[(1~{S})-1-phenylethyl]ethanamide
  • Ligand: water
KeywordsGPR139 / Complex / G protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


neuropeptide receptor activity / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / D1 dopamine receptor binding / intracellular transport / vascular endothelial cell response to laminar fluid shear stress ...neuropeptide receptor activity / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / D1 dopamine receptor binding / intracellular transport / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of insulin secretion / cellular response to glucagon stimulus / adenylate cyclase activator activity / trans-Golgi network membrane / negative regulation of inflammatory response to antigenic stimulus / bone development / platelet aggregation / cognition / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / sensory perception of smell / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events / extracellular vesicle / sensory perception of taste / positive regulation of cold-induced thermogenesis / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / G protein activity / retina development in camera-type eye / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / GTP binding / protein-containing complex binding / signal transduction / extracellular exosome / metal ion binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
G-protein-coupled receptor GPR139 / : / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. ...G-protein-coupled receptor GPR139 / : / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Concanavalin A-like lectin/glucanase domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Endo-1,4-beta-xylanase / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Probable G-protein coupled receptor 139
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCabezadevaca I / Trapkov B / Shen L / Pezeshki M / Zhang XH / Liu Z / Hauser AS / Carlsson J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Ultra-large virtual screening unveils potent agonists of the neuromodulatory orphan receptor GPR139.
Authors: Israel Cabeza de Vaca / Boris Trapkov / Ling Shen / Duy Duc Vo / Xiaoqun Zhang / Yunting Yang / Mitra Pezeshki / Xuehan Zhang / Frida Bällgren / Aljona Saleh / Andrii V Tarnovskiy / Dmytro ...Authors: Israel Cabeza de Vaca / Boris Trapkov / Ling Shen / Duy Duc Vo / Xiaoqun Zhang / Yunting Yang / Mitra Pezeshki / Xuehan Zhang / Frida Bällgren / Aljona Saleh / Andrii V Tarnovskiy / Dmytro S Radchenko / Yurii S Moroz / Hans Bräuner-Osborne / Per Svenningsson / Jan Kihlberg / Zhi-Jie Liu / Alexander Sebastian Hauser / Jens Carlsson /
Abstract: The orphan G protein-coupled receptor (GPCR) GPR139 attracts interest as a target for neuropsychiatric disorders. Whereas the physiological functions of GPR139 remain elusive, a high-resolution ...The orphan G protein-coupled receptor (GPCR) GPR139 attracts interest as a target for neuropsychiatric disorders. Whereas the physiological functions of GPR139 remain elusive, a high-resolution receptor structure is now available. To assess whether structural information enables ligand discovery, we computationally dock 235 million compounds to the GPR139 binding site. Of 68 top-ranked compounds evaluated experimentally, five are full agonists with potencies ranging from 160 nM to 3.6 µM. Structure-guided optimization identifies one of the most potent GPR139 agonists, and a cryo-EM structure of the receptor-ligand complex confirms the predicted binding mode. Functional characterization provides insights into GPR139 signalling, and one agonist elicits behavioural effects in mice. We also explore the potential to replace experimental structure determination with the deep-learning method AlphaFold3, revealing a limited capability of artificial intelligence to model receptor-ligand interactions for understudied GPCRs. The results demonstrate how high-resolution GPCR structures combined with large-library docking can accelerate drug discovery.
History
DepositionMar 3, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63614.png

Downloads & links

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Map

FileDownload / File: emd_63614.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0017742519 - 2.2783115
Average (Standard dev.)0.0013166256 (±0.028084137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63614_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_63614_half_map_2.map
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Sample components

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Entire : GPR139_Gs/q

EntireName: GPR139_Gs/q
Components
  • Complex: GPR139_Gs/q
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Nanobody 35
    • Protein or peptide: Endo-1,4-beta-xylanase,Probable G-protein coupled receptor 139
  • Ligand: 2-[5-(4-methylthiophen-3-yl)-1,2,4-oxadiazol-3-yl]-~{N}-[(1~{S})-1-phenylethyl]ethanamide
  • Ligand: water

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Supramolecule #1: GPR139_Gs/q

SupramoleculeName: GPR139_Gs/q / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.59551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQGNSKTED QRNEEKAQRE ANKKIEKQLQ KDKQVYRATH RLLLLGADNS GKSTIVKQMR ILHGGSGGSG GTSGIFETK FQVDKVNFHM FDVGGQRDER RKWIQCFNDV TAIIFVVDSS DYNRLQEALN LFKSIWNNRW LRTISVILFL N KQDLLAEK ...String:
MHHHHHHENL YFQGNSKTED QRNEEKAQRE ANKKIEKQLQ KDKQVYRATH RLLLLGADNS GKSTIVKQMR ILHGGSGGSG GTSGIFETK FQVDKVNFHM FDVGGQRDER RKWIQCFNDV TAIIFVVDSS DYNRLQEALN LFKSIWNNRW LRTISVILFL N KQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRDEFLRIST ASGDGRHYCY PHFTCAVDTE NA RRIFNDC KDIILQMNLR EYNLV

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.564102 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FMSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGKL IIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC CRFLDDNQIV T SSGDTTCA ...String:
FMSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGKL IIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC CRFLDDNQIV T SSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DINAICFFPN GN AFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDALKADRAG VLAGHDNRVS CLG VTDDGM AVATGSWDSF LKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.49796 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MHHHHHHGGG SDSLEFIASK LAGGGSMASN NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFRE KKFFSAIL

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.483693 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAMQVQLQES GGGLVQPGGS LRLSCAASGF TFSNYKMNWV RQAPGKGLEW VSDISQSGAS ISYTGSVKG RFTISRDNAK NTLYLQMNSL KPEDTAVYYC ARCPAPFTRD CFDVTSTTYA YRGQGTQVTV SSHHHHHHEP E A

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Macromolecule #5: Endo-1,4-beta-xylanase,Probable G-protein coupled receptor 139

MacromoleculeName: Endo-1,4-beta-xylanase,Probable G-protein coupled receptor 139
type: protein_or_peptide / ID: 5
Details: Chimera of Endo-1,4-beta-xylanase and Probable G-protein coupled receptor 139
Number of copies: 1 / Enantiomer: LEVO / EC number: endo-1,4-beta-xylanase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.964281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKHHHHHHHH HHDYKDDDDA ENLYFQSPAS TDYWQNWTFG GGIVNAVNGS GGNYSVNWSN TGNFVVGKGW TTGSPFRTIN YNAGVWAPN GNGYLTLYGW TRSPLIEYYV VDSWGTYRPT GTYKGTVKSD GGTYDIYTTT RYNAPSIDGD DTTFTQYWSV R QSKRPTGS ...String:
MKHHHHHHHH HHDYKDDDDA ENLYFQSPAS TDYWQNWTFG GGIVNAVNGS GGNYSVNWSN TGNFVVGKGW TTGSPFRTIN YNAGVWAPN GNGYLTLYGW TRSPLIEYYV VDSWGTYRPT GTYKGTVKSD GGTYDIYTTT RYNAPSIDGD DTTFTQYWSV R QSKRPTGS NATITFTNHV NAWKSHGMNL GSNWAYQVMA TEGYQSSGSS NVTVWEHTHA HLAANSSLSW WSPGSACGLG FV PVVYYSL LLCLGLPANI LTVIILSQLV ARRQKSVYNY LLALAAADIL VLFFIVFVDF LLEDFILNMQ MPQVPDKIIE VLE FSSIHT SIWITVPLTI DRYIAVCHPL KYHTVSYPAR TRKVIVSVYI TCFLTSIPYY WWPNIWTEDY ISTSVHHVLI WIHC FTVYL VPCSIFFILN SIIVYKLRRK SNFRLRGYST GKTTAILFTI TSIFATLWAP RIIMILYHLY GAPIQNRWLV HIMSD IANM LALLNTAINF FLYCFISKRF RTMAAATLKA FFKCQKQPVQ FYTNHNFSI

UniProtKB: Endo-1,4-beta-xylanase, Probable G-protein coupled receptor 139

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Macromolecule #6: 2-[5-(4-methylthiophen-3-yl)-1,2,4-oxadiazol-3-yl]-~{N}-[(1~{S})-...

MacromoleculeName: 2-[5-(4-methylthiophen-3-yl)-1,2,4-oxadiazol-3-yl]-~{N}-[(1~{S})-1-phenylethyl]ethanamide
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1L8O
Molecular weightTheoretical: 327.401 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 138265
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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