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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2009-01-29 16:43:01 UTC

Update Date

2021-09-14 15:45:11 UTC

HMDB ID

HMDB0011622

Secondary Accession Numbers

HMDB11622

Metabolite Identification

Common Name

D-Dopachrome

Description

D-dopachrome is reversibly converted into 5,6-dihydroxyindole and carbon dioxide via the enzyme D-dopachrome decarboxylase (EC 4.1.1.84). Cultured human melanoma cells contain this enzyme as well as human liver (PMID: 8267597 ). Dopaquinone has an ortho-quinone ring, which is known to be neurotoxic and highly reactive with many other compounds (PMID: 413870 ).

Structure

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


  Mrv1652303051804482D          

 14 15  0  0  0  0            999 V2000
 9997.5010 9998.7614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.501010000.4128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.932610000.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.218110000.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2181 9999.1749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9326 9998.7625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.431610000.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6471 9999.9999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6470 9999.1749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.4316 9998.9200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.9165 9999.5874    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10001.7415 9999.5874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.1540 9998.8729    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.154110000.3018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  1  0  0  0
 12 14  2  0  0  0  0
 12 13  1  0  0  0  0
  5  1  2  0  0  0  0
  4  2  2  0  0  0  0
  3  8  2  0  0  0  0
  6  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0011622

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H7NO4/c11-7-2-4-1-6(9(13)14)10-5(4)3-8(7)12/h2-3,6,10H,1H2,(H,13,14)/t6-/m1/s1

> <INCHI_KEY>
VJNCICVKUHKIIV-ZCFIWIBFSA-N

> <FORMULA>
C9H7NO4

> <MOLECULAR_WEIGHT>
193.158

> <EXACT_MASS>
193.037507709

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
17.530328232223557

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R)-5,6-dioxo-2,3,5,6-tetrahydro-1H-indole-2-carboxylic acid

> <ALOGPS_LOGP>
0.22

> <JCHEM_LOGP>
-0.08718718499999992

> <ALOGPS_LOGS>
-1.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.0573667859171

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.668581054597647

> <JCHEM_PKA_STRONGEST_BASIC>
-8.82531687301901

> <JCHEM_POLAR_SURFACE_AREA>
83.47

> <JCHEM_REFRACTIVITY>
47.883700000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.02e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-dopachrome

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-MAR-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-MAR-18         0                                  
HETATM    1  O   UNK     0    8662.0028664.355   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8662.0028667.437   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    8664.6748667.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8663.3408666.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8663.3408665.126   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8664.6748664.357   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0    8667.4728667.142   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0    8666.0088666.666   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8666.0088665.126   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8667.4728664.651   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8668.3778665.896   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8669.9178665.896   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0    8670.6878664.563   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0    8670.6888667.230   0.000  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    4                                                            
CONECT    3    4    8                                                       
CONECT    4    3    5    2                                                  
CONECT    5    4    6    1                                                  
CONECT    6    5    9                                                       
CONECT    7    8   11                                                       
CONECT    8    9    7    3                                                  
CONECT    9    8   10    6                                                  
CONECT   10    9   11                                                       
CONECT   11   10    7   12                                                  
CONECT   12   11   14   13                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₉H₇NO₄

Average Molecular Weight

193.158

Monoisotopic Molecular Weight

193.037507709

IUPAC Name

(2R)-5,6-dioxo-2,3,5,6-tetrahydro-1H-indole-2-carboxylic acid

Traditional Name

D-dopachrome

CAS Registry Number

203000-17-3

SMILES

OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1

InChI Identifier

InChI=1S/C9H7NO4/c11-7-2-4-1-6(9(13)14)10-5(4)3-8(7)12/h2-3,6,10H,1H2,(H,13,14)/t6-/m1/s1

InChI Key

VJNCICVKUHKIIV-ZCFIWIBFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-alpha-amino acids

Alternative Parents

Substituents

D-alpha-amino acid
Indole or derivatives
Dihydroindole
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Pyrrolidine
Vinylogous amide
Amino acid
Ketone
Cyclic ketone
Carboxylic acid
Secondary aliphatic amine
Enamine
Monocarboxylic acid or derivatives
Azacycle
Secondary amine
Organoheterocyclic compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Amine
Hydrocarbon derivative
Carbonyl group
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

dopachrome (CHEBI:49109 )

Ontology

Not Available

Physical Properties

State

Solid

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
Water Solubility	10.2 g/L	ALOGPS
logP	0.22	ALOGPS
logP	-0.087	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	3.67	ChemAxon
pKa (Strongest Basic)	-8.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.47 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	47.88 m³·mol⁻¹	ChemAxon
Polarizability	17.53 Å³	ChemAxon
Number of Rings	2	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
DarkChem	[M+H]+	142.811	31661259
DarkChem	[M-H]-	138.807	31661259
DeepCCS	[M+H]+	139.693	30932474
DeepCCS	[M-H]-	137.297	30932474
DeepCCS	[M-2H]-	170.999	30932474
DeepCCS	[M+Na]+	145.688	30932474
AllCCS	[M+H]+	141.3	32859911
AllCCS	[M+H-H2O]+	137.0	32859911
AllCCS	[M+NH4]+	145.3	32859911
AllCCS	[M+Na]+	146.4	32859911
AllCCS	[M-H]-	138.6	32859911
AllCCS	[M+Na-2H]-	138.8	32859911
AllCCS	[M+HCOO]-	139.0	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
D-Dopachrome	OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1	3410.4	Standard polar	33892256
D-Dopachrome	OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1	1679.3	Standard non polar	33892256
D-Dopachrome	OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1	2079.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
D-Dopachrome,1TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1	2148.2	Semi standard non polar	33892256
D-Dopachrome,1TMS,isomer #2	C[Si](C)(C)N1C2=CC(=O)C(=O)C=C2C[C@@H]1C(=O)O	2208.2	Semi standard non polar	33892256
D-Dopachrome,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1[Si](C)(C)C	2204.9	Semi standard non polar	33892256
D-Dopachrome,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1[Si](C)(C)C	1933.8	Standard non polar	33892256
D-Dopachrome,2TMS,isomer #1	C[Si](C)(C)OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1[Si](C)(C)C	3214.0	Standard polar	33892256
D-Dopachrome,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1	2399.8	Semi standard non polar	33892256
D-Dopachrome,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N1C2=CC(=O)C(=O)C=C2C[C@@H]1C(=O)O	2455.4	Semi standard non polar	33892256
D-Dopachrome,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1[Si](C)(C)C(C)(C)C	2665.8	Semi standard non polar	33892256
D-Dopachrome,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1[Si](C)(C)C(C)(C)C	2361.6	Standard non polar	33892256
D-Dopachrome,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CC2=CC(=O)C(=O)C=C2N1[Si](C)(C)C(C)(C)C	3349.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - D-Dopachrome GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Dopachrome GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 10V, Positive-QTOF	splash10-002f-0900000000-7d241073b22105a8fd50	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 20V, Positive-QTOF	splash10-0002-0900000000-323f4bcd8528fb467c2b	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 40V, Positive-QTOF	splash10-00ba-7900000000-13c63b10c546db28b452	2019-02-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 10V, Negative-QTOF	splash10-0006-0900000000-7278b78e7703333d1049	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 20V, Negative-QTOF	splash10-006w-0900000000-37fa92b16a4a5557156c	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 40V, Negative-QTOF	splash10-006w-2900000000-a811e0992f3245b7b855	2019-02-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 10V, Negative-QTOF	splash10-0006-0900000000-becbc589150d5f7b8591	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 20V, Negative-QTOF	splash10-0002-0900000000-96e2a94dd742e6e1937c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 40V, Negative-QTOF	splash10-006w-1900000000-1956f467b1b38dab6842	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 10V, Positive-QTOF	splash10-0006-0900000000-ae6d437a06113eb43338	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 20V, Positive-QTOF	splash10-004m-0900000000-5329f1d5b80270050bbb	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Dopachrome 40V, Positive-QTOF	splash10-006y-8900000000-bfc43ab0afc8b1b28daf	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

FDB028326

KNApSAcK ID

Not Available

Chemspider ID

21865634

KEGG Compound ID

C15566

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dopachrome

METLIN ID

Not Available

PubChem Compound

24771780

PDB ID

Not Available

ChEBI ID

49109

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

Odh G, Hindemith A, Rosengren AM, Rosengren E, Rorsman H: Isolation of a new tautomerase monitored by the conversion of D-dopachrome to 5,6-dihydroxyindole. Biochem Biophys Res Commun. 1993 Dec 15;197(2):619-24. [PubMed:8267597 ]
Graham DG, Tiffany SM, Vogel FS: The toxicity of melanin precursors. J Invest Dermatol. 1978 Feb;70(2):113-6. [PubMed:413870 ]

Enzymes

Enzyme Details

1. D-dopachrome decarboxylase

General function:: Involved in D-dopachrome decarboxylase activity
Specific function:: Tautomerization of D-dopachrome with decarboxylation to give 5,6-dihydroxyindole (DHI).
Gene Name:: DDT
Uniprot ID:: P30046
Molecular weight:: 12711.605

Reactions

D-Dopachrome → 5,6-Dihydroxyindole + CO(2)	details

Showing metabocard for D-Dopachrome (HMDB0011622)

MOL for HMDB0011622 (D-Dopachrome)

3D MOL for HMDB0011622 (D-Dopachrome)

3D SDF for HMDB0011622 (D-Dopachrome)

3D-SDF for HMDB0011622 (D-Dopachrome)

PDB for HMDB0011622 (D-Dopachrome)

3D PDB for HMDB0011622 (D-Dopachrome)

SMILES for HMDB0011622 (D-Dopachrome)

INCHI for HMDB0011622 (D-Dopachrome)

Structure for HMDB0011622 (D-Dopachrome)

3D Structure for HMDB0011622 (D-Dopachrome)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions