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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 14:15:28 UTC

Update Date

2021-09-26 23:09:05 UTC

HMDB ID

HMDB0254807

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one

Description

3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one belongs to the class of organic compounds known as indolines. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene to form 2,3-dihydroindole. Based on a literature review very few articles have been published on 3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-(1h-imidazol-5-ylmethylene)-1,3-dihydro-2h-indol-2-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652309112116152D          

 16 18  0  0  0  0            999 V2000
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358    3.5881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2643    4.3951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9788    4.8076    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5919    4.2555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2563    3.5019    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   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
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  4  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
  9 13  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
  4 16  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0254807

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1NC2=CC=CC=C2C1=CC1=CN=CN1

> <INCHI_IDENTIFIER>
InChI=1S/C12H9N3O/c16-12-10(5-8-6-13-7-14-8)9-3-1-2-4-11(9)15-12/h1-7H,(H,13,14)(H,15,16)

> <INCHI_KEY>
VEEGZPWAAPPXRB-UHFFFAOYSA-N

> <FORMULA>
C12H9N3O

> <MOLECULAR_WEIGHT>
211.224

> <EXACT_MASS>
211.074561922

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
21.807143228490908

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[(1H-imidazol-5-yl)methylidene]-2,3-dihydro-1H-indol-2-one

> <ALOGPS_LOGP>
1.23

> <JCHEM_LOGP>
1.0667612376666669

> <ALOGPS_LOGS>
-2.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.773529788173587

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.247884056951394

> <JCHEM_PKA_STRONGEST_BASIC>
6.63743005020136

> <JCHEM_POLAR_SURFACE_AREA>
57.78

> <JCHEM_REFRACTIVITY>
62.563599999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.57e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(3H-imidazol-4-ylmethylidene)-1H-indol-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

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       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.650   5.553   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.680   6.698   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.360   8.204   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       3.694   8.974   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       4.838   7.944   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.212   6.537   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.320   2.843   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   16                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   14                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    9                                                       
CONECT   14    7   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14    4                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

COMPND    HMDB0254807
HETATM    1  O1  UNL     1       1.284   2.227  -0.077  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.220   1.564  -0.025  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.089   2.115   0.012  1.00  0.00           N  
HETATM    4  C2  UNL     1      -1.988   1.035   0.063  1.00  0.00           C  
HETATM    5  C3  UNL     1      -3.378   1.001   0.112  1.00  0.00           C  
HETATM    6  C4  UNL     1      -4.075  -0.185   0.157  1.00  0.00           C  
HETATM    7  C5  UNL     1      -3.392  -1.382   0.154  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.011  -1.349   0.105  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.310  -0.165   0.060  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.141   0.118   0.004  1.00  0.00           C  
HETATM   11  C9  UNL     1       1.069  -0.800   0.002  1.00  0.00           C  
HETATM   12  C10 UNL     1       2.504  -0.510  -0.027  1.00  0.00           C  
HETATM   13  C11 UNL     1       3.155   0.333   0.837  1.00  0.00           C  
HETATM   14  N2  UNL     1       4.445   0.388   0.508  1.00  0.00           N  
HETATM   15  C12 UNL     1       4.582  -0.428  -0.564  1.00  0.00           C  
HETATM   16  N3  UNL     1       3.418  -0.973  -0.891  1.00  0.00           N  
HETATM   17  H1  UNL     1      -1.319   3.112   0.002  1.00  0.00           H  
HETATM   18  H2  UNL     1      -3.885   1.954   0.112  1.00  0.00           H  
HETATM   19  H3  UNL     1      -5.169  -0.197   0.194  1.00  0.00           H  
HETATM   20  H4  UNL     1      -3.943  -2.328   0.190  1.00  0.00           H  
HETATM   21  H5  UNL     1      -1.459  -2.299   0.104  1.00  0.00           H  
HETATM   22  H6  UNL     1       0.764  -1.859   0.026  1.00  0.00           H  
HETATM   23  H7  UNL     1       2.705   0.876   1.687  1.00  0.00           H  
HETATM   24  H8  UNL     1       5.528  -0.600  -1.071  1.00  0.00           H  
HETATM   25  H9  UNL     1       3.203  -1.647  -1.677  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4   17
CONECT    4    5    5    9
CONECT    5    6   18
CONECT    6    7    7   19
CONECT    7    8   20
CONECT    8    9    9   21
CONECT    9   10
CONECT   10   11   11
CONECT   11   12   22
CONECT   12   13   13   16
CONECT   13   14   23
CONECT   14   15   15
CONECT   15   16   24
CONECT   16   25
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₂H₉N₃O

Average Molecular Weight

211.224

Monoisotopic Molecular Weight

211.074561922

IUPAC Name

3-[(1H-imidazol-5-yl)methylidene]-2,3-dihydro-1H-indol-2-one

Traditional Name

3-(3H-imidazol-4-ylmethylidene)-1H-indol-2-one

CAS Registry Number

Not Available

SMILES

O=C1NC2=CC=CC=C2C1=CC1=CN=CN1

InChI Identifier

InChI=1S/C12H9N3O/c16-12-10(5-8-6-13-7-14-8)9-3-1-2-4-11(9)15-12/h1-7H,(H,13,14)(H,15,16)

InChI Key

VEEGZPWAAPPXRB-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolines. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene to form 2,3-dihydroindole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indolines

Direct Parent

Indolines

Alternative Parents

Substituents

Dihydroindole
Benzenoid
Azole
Imidazole
Heteroaromatic compound
Carboxamide group
Lactam
Secondary carboxylic acid amide
Carboxylic acid derivative
Azacycle
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Organooxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	1.23	ALOGPS
logP	1.07	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	11.25	ChemAxon
pKa (Strongest Basic)	6.64	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.78 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	62.56 m³·mol⁻¹	ChemAxon
Polarizability	21.81 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	140.705	30932474
DeepCCS	[M-H]-	138.309	30932474
DeepCCS	[M-2H]-	172.524	30932474
DeepCCS	[M+Na]+	146.95	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one	O=C1NC2=CC=CC=C2C1=CC1=CN=CN1	3523.8	Standard polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one	O=C1NC2=CC=CC=C2C1=CC1=CN=CN1	2641.5	Standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one	O=C1NC2=CC=CC=C2C1=CC1=CN=CN1	2676.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TMS,isomer #1	C[Si](C)(C)N1C(=O)C(=CC2=CN=C[NH]2)C2=CC=CC=C21	2387.6	Semi standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TMS,isomer #1	C[Si](C)(C)N1C(=O)C(=CC2=CN=C[NH]2)C2=CC=CC=C21	2194.0	Standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TMS,isomer #1	C[Si](C)(C)N1C(=O)C(=CC2=CN=C[NH]2)C2=CC=CC=C21	3082.8	Standard polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TMS,isomer #2	C[Si](C)(C)N1C=NC=C1C=C1C(=O)NC2=CC=CC=C12	2516.8	Semi standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TMS,isomer #2	C[Si](C)(C)N1C=NC=C1C=C1C(=O)NC2=CC=CC=C12	2427.5	Standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TMS,isomer #2	C[Si](C)(C)N1C=NC=C1C=C1C(=O)NC2=CC=CC=C12	3456.5	Standard polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,2TMS,isomer #1	C[Si](C)(C)N1C(=O)C(=CC2=CN=CN2[Si](C)(C)C)C2=CC=CC=C21	2454.8	Semi standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,2TMS,isomer #1	C[Si](C)(C)N1C(=O)C(=CC2=CN=CN2[Si](C)(C)C)C2=CC=CC=C21	2352.0	Standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,2TMS,isomer #1	C[Si](C)(C)N1C(=O)C(=CC2=CN=CN2[Si](C)(C)C)C2=CC=CC=C21	2865.4	Standard polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)C(=CC2=CN=C[NH]2)C2=CC=CC=C21	2651.0	Semi standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)C(=CC2=CN=C[NH]2)C2=CC=CC=C21	2411.5	Standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)C(=CC2=CN=C[NH]2)C2=CC=CC=C21	3175.1	Standard polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C=NC=C1C=C1C(=O)NC2=CC=CC=C12	2756.5	Semi standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C=NC=C1C=C1C(=O)NC2=CC=CC=C12	2641.4	Standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C=NC=C1C=C1C(=O)NC2=CC=CC=C12	3546.7	Standard polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)C(=CC2=CN=CN2[Si](C)(C)C(C)(C)C)C2=CC=CC=C21	2900.0	Semi standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)C(=CC2=CN=CN2[Si](C)(C)C(C)(C)C)C2=CC=CC=C21	2769.8	Standard non polar	33892256
3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N1C(=O)C(=CC2=CN=CN2[Si](C)(C)C(C)(C)C)C2=CC=CC=C21	3019.3	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one GC-MS (Non-derivatized) - 70eV, Positive	splash10-01q9-0920000000-9b87679b32e026487577	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

2090579

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

2812173

PDB ID

Not Available

ChEBI ID

92147

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for 3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one (HMDB0254807)

MOL for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

3D MOL for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

3D SDF for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

3D-SDF for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

PDB for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

3D PDB for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

SMILES for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

INCHI for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

Structure for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

3D Structure for HMDB0254807 (3-(1H-Imidazol-5-ylmethylene)-1,3-dihydro-2H-indol-2-one)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra