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Showing metabocard for Imidazo[1,2-a]pyridine (HMDB0253414)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 11:51:09 UTC
Update Date2021-09-26 23:06:37 UTC
HMDB IDHMDB0253414
Secondary Accession NumbersNone
Metabolite Identification
Common NameImidazo[1,2-a]pyridine
DescriptionImidazo[1,2-a]pyridine belongs to the class of organic compounds known as imidazopyridines. These are organic polycyclic compounds containing an imidazole ring fused to a pyridine ring. Imidazole is 5-membered ring consisting of three carbon atoms, and two nitrogen centers at the 1- and 3-positions. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center. Based on a literature review a significant number of articles have been published on Imidazo[1,2-a]pyridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Imidazo[1,2-a]pyridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Imidazo[1,2-a]pyridine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0253414 (Imidazo[1,2-a]pyridine)


  Mrv1652309112113512D          

  9 10  0  0  0  0            999 V2000
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  1  9  1  0  0  0  0
M  END
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3D MOL for HMDB0253414 (Imidazo[1,2-a]pyridine)

HMDB0253414
     RDKit          3D
Imidazo[1,2-a]pyridine
 15 16  0  0  0  0  0  0  0  0999 V2000
   -2.0463   -0.6220    0.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8840    0.7463    0.0468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5928    1.2689   -0.0342 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4979    0.4780   -0.0443 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8346    0.7566   -0.1157 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5342   -0.4312   -0.0900 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6114   -1.4036   -0.0038 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3683   -0.8614    0.0247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9128   -1.4085    0.1063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0423   -1.0428    0.1818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7399    1.4157    0.0524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4396    2.3374   -0.0914 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2469    1.7550   -0.1808 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6086   -0.5127   -0.1329 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0442   -2.4757    0.1625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9  1  2  0
  8  4  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  9 15  1  0
M  END
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3D SDF for HMDB0253414 (Imidazo[1,2-a]pyridine)


  Mrv1652309112113512D          

  9 10  0  0  0  0            999 V2000
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  1  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253414

> <DATABASE_NAME>
hmdb

> <SMILES>
C1=CN2C=CC=CC2=N1

> <INCHI_IDENTIFIER>
InChI=1S/C7H6N2/c1-2-5-9-6-4-8-7(9)3-1/h1-6H

> <INCHI_KEY>
UTCSSFWDNNEEBH-UHFFFAOYSA-N

> <FORMULA>
C7H6N2

> <MOLECULAR_WEIGHT>
118.139

> <EXACT_MASS>
118.053098201

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
12.200059163824458

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
imidazo[1,2-a]pyridine

> <ALOGPS_LOGP>
1.24

> <JCHEM_LOGP>
0.7595494243333332

> <ALOGPS_LOGS>
-0.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
6.598800230507331

> <JCHEM_POLAR_SURFACE_AREA>
17.3

> <JCHEM_REFRACTIVITY>
35.93639999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.95e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
imidazo[1,2-a]pyridine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0253414 (Imidazo[1,2-a]pyridine)

HMDB0253414
     RDKit          3D
Imidazo[1,2-a]pyridine
 15 16  0  0  0  0  0  0  0  0999 V2000
   -2.0463   -0.6220    0.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8840    0.7463    0.0468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5928    1.2689   -0.0342 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4979    0.4780   -0.0443 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8346    0.7566   -0.1157 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5342   -0.4312   -0.0900 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6114   -1.4036   -0.0038 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3683   -0.8614    0.0247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9128   -1.4085    0.1063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0423   -1.0428    0.1818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7399    1.4157    0.0524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4396    2.3374   -0.0914 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2469    1.7550   -0.1808 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6086   -0.5127   -0.1329 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0442   -2.4757    0.1625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9  1  2  0
  8  4  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  9 15  1  0
M  END
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PDB for HMDB0253414 (Imidazo[1,2-a]pyridine)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -0.268   1.597   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.268   4.089   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.197   3.613   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.864   3.613   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8    1                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   20    0
END
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3D PDB for HMDB0253414 (Imidazo[1,2-a]pyridine)

COMPND    HMDB0253414
HETATM    1  C1  UNL     1      -2.046  -0.622   0.119  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.884   0.746   0.047  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.593   1.269  -0.034  1.00  0.00           C  
HETATM    4  N1  UNL     1       0.498   0.478  -0.044  1.00  0.00           N  
HETATM    5  C4  UNL     1       1.835   0.757  -0.116  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.534  -0.431  -0.090  1.00  0.00           C  
HETATM    7  N2  UNL     1       1.611  -1.404  -0.004  1.00  0.00           N  
HETATM    8  C6  UNL     1       0.368  -0.861   0.025  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.913  -1.409   0.106  1.00  0.00           C  
HETATM   10  H1  UNL     1      -3.042  -1.043   0.182  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.740   1.416   0.052  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.440   2.337  -0.091  1.00  0.00           H  
HETATM   13  H4  UNL     1       2.247   1.755  -0.181  1.00  0.00           H  
HETATM   14  H5  UNL     1       3.609  -0.513  -0.133  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.044  -2.476   0.163  1.00  0.00           H  
CONECT    1    2    9    9   10
CONECT    2    3    3   11
CONECT    3    4   12
CONECT    4    5    8
CONECT    5    6    6   13
CONECT    6    7   14
CONECT    7    8    8
CONECT    8    9
CONECT    9   15
END
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SMILES for HMDB0253414 (Imidazo[1,2-a]pyridine)

C1=CN2C=CC=CC2=N1
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INCHI for HMDB0253414 (Imidazo[1,2-a]pyridine)

InChI=1S/C7H6N2/c1-2-5-9-6-4-8-7(9)3-1/h1-6H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Imidazo(1,2-a)pyridineHMDB
Chemical FormulaC7H6N2
Average Molecular Weight118.139
Monoisotopic Molecular Weight118.053098201
IUPAC Nameimidazo[1,2-a]pyridine
Traditional Nameimidazo[1,2-a]pyridine
CAS Registry NumberNot Available
SMILES
C1=CN2C=CC=CC2=N1
InChI Identifier
InChI=1S/C7H6N2/c1-2-5-9-6-4-8-7(9)3-1/h1-6H
InChI KeyUTCSSFWDNNEEBH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as imidazopyridines. These are organic polycyclic compounds containing an imidazole ring fused to a pyridine ring. Imidazole is 5-membered ring consisting of three carbon atoms, and two nitrogen centers at the 1- and 3-positions. Pyridine is a 6-membered ring consisting of five carbon atoms and one nitrogen center.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassImidazopyridines
Sub ClassNot Available
Direct ParentImidazopyridines
Alternative Parents
Substituents
  • Imidazo[1,2-a]pyridine
  • Imidazopyridine
  • Pyridine
  • N-substituted imidazole
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.24ALOGPS
logP0.76ChemAxon
logS-0.23ALOGPS
pKa (Strongest Basic)6.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.3 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity35.94 m³·mol⁻¹ChemAxon
Polarizability12.2 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+121.61330932474
DeepCCS[M-H]-118.28930932474
DeepCCS[M-2H]-155.27330932474
DeepCCS[M+Na]+130.21930932474
AllCCS[M+H]+122.432859911
AllCCS[M+H-H2O]+117.432859911
AllCCS[M+NH4]+127.232859911
AllCCS[M+Na]+128.632859911
AllCCS[M-H]-119.832859911
AllCCS[M+Na-2H]-121.332859911
AllCCS[M+HCOO]-123.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.6307 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.48 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid922.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid309.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid89.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid198.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid52.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid260.1 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid264.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)98.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid615.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid40.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid825.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid182.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid231.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate462.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA277.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water172.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Imidazo[1,2-a]pyridineC1=CN2C=CC=CC2=N11726.8Standard polar33892256
Imidazo[1,2-a]pyridineC1=CN2C=CC=CC2=N11357.2Standard non polar33892256
Imidazo[1,2-a]pyridineC1=CN2C=CC=CC2=N11297.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Imidazo[1,2-a]pyridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-6900000000-c00dbf95b55e2c8ef47b2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Imidazo[1,2-a]pyridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Imidazo[1,2-a]pyridine 10V, Negative-QTOFsplash10-014i-0900000000-6e1aa709126082eacb982021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Imidazo[1,2-a]pyridine 20V, Negative-QTOFsplash10-014i-0900000000-6e1aa709126082eacb982021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Imidazo[1,2-a]pyridine 40V, Negative-QTOFsplash10-014i-2900000000-67e1ff9d44621c585a1f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Imidazo[1,2-a]pyridine 10V, Positive-QTOFsplash10-014i-0900000000-b264926dd01c80902ad82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Imidazo[1,2-a]pyridine 20V, Positive-QTOFsplash10-014i-0900000000-b264926dd01c80902ad82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Imidazo[1,2-a]pyridine 40V, Positive-QTOFsplash10-0udi-9000000000-16b867f28ed3f267e1752021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID71293
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound78960
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]