MiMeDB: Showing metabocard for 5,10-Methenyl-5,6,7,8-tetrahydromethanopterin (MMDBc0048048)

Microbial

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-04-29 21:46:55 UTC

Update Date

2025-10-07 16:08:10 UTC

Metabolite ID

MMDBc0048048

Metabolite Identification

Common Name

5,10-Methenyl-5,6,7,8-tetrahydromethanopterin

Description

5,10-Methenyl-5,6,7,8-tetrahydromethanopterin is a member of the pterin chemical class, specifically a derivative of tetrahydromethanopterin. Its chemical structure features a methenyl group at the 5 and 10 positions, contributing to its role as a crucial intermediate in various biochemical pathways, particularly in the reduction of carbon dioxide to methane. This compound is involved in methanogenesis, a biological process carried out by methanogenic archaea, where it serves as a cofactor in the enzymatic reactions that facilitate the conversion of CO2 into methane. Notably, during purification procedures, 5,10-methenyl-5,6,7,8-tetrahydromethanopterin can degrade to form 6-acetyl-7-methyl-7,8-dihydropterin, as identified in studies (PMID:6703711 ). Additionally, upon aerobic heating with alkali, it produces a green-yellow fluorescent degradation product, indicating its chemical reactivity and stability under varying conditions (PMID:6703711 ). This highlights the compound's significance in both metabolic pathways and its potential for chemical transformations.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041403142D          

 65 69  0  0  1  0            999 V2000
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M  CHG  1  36   1
M  END


  Mrv0541 05041403142D          

 65 69  0  0  1  0            999 V2000
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M  CHG  1  36   1
M  END
> <DATABASE_ID>
MMDBc0048048

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CO[C@@]1([H])O[C@]([H])(COP(O)(=O)O[C@@]([H])(CCC(O)=O)C(O)=O)[C@@]([H])(O)[C@@]1([H])O)[C@@]([H])(O)[C@@]([H])(O)CC1=CC=C(C=C1)[N+]1=CN2C3=C(NC(=N)N=C3O)N[C@@]([H])(C)[C@]2([H])[C@@]1([H])C

> <INCHI_IDENTIFIER>
InChI=1S/C31H43N6O16P/c1-13-22-14(2)36(12-37(22)23-27(33-13)34-31(32)35-28(23)45)16-5-3-15(4-6-16)9-17(38)24(42)18(39)10-50-30-26(44)25(43)20(52-30)11-51-54(48,49)53-19(29(46)47)7-8-21(40)41/h3-6,12-14,17-20,22,24-26,30,38-39,42-44H,7-11H2,1-2H3,(H6-,32,33,34,35,40,41,45,46,47,48,49)/p+1/t13-,14+,17-,18+,19-,20+,22+,24-,25+,26+,30-/m0/s1

> <INCHI_KEY>
RANKJVUGLXUXOL-CAFBYHECSA-O

> <FORMULA>
C31H44N6O16P

> <MOLECULAR_WEIGHT>
787.6854

> <EXACT_MASS>
787.255140902

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
77.15739361490425

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6S,6aR,7R)-8-{4-[(2S,3S,4R)-5-{[(2S,3R,4S,5R)-5-[({[(1S)-1,3-dicarboxypropoxy](hydroxy)phosphoryl}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]oxy}-2,3,4-trihydroxypentyl]phenyl}-1-hydroxy-3-imino-6,7-dimethyl-3H,4H,5H,6H,6aH,7H-8λ⁵-imidazo[1,5-f]pteridin-8-ylium

> <ALOGPS_LOGP>
-1.42

> <JCHEM_LOGP>
-7.947104233926167

> <ALOGPS_LOGS>
-3.76

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
1.7484316082553661

> <JCHEM_PKA_STRONGEST_ACIDIC>
-2.664223227052326

> <JCHEM_PKA_STRONGEST_BASIC>
15.001026813028206

> <JCHEM_POLAR_SURFACE_AREA>
336.72

> <JCHEM_REFRACTIVITY>
210.59260000000012

> <JCHEM_ROTATABLE_BOND_COUNT>
17

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.43e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6S,6aR,7R)-8-{4-[(2S,3S,4R)-5-{[(2S,3R,4S,5R)-5-({[(1S)-1,3-dicarboxypropoxy(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]oxy}-2,3,4-trihydroxypentyl]phenyl}-1-hydroxy-3-imino-6,7-dimethyl-4H,5H,6H,6aH,7H-8λ⁵-imidazo[1,5-f]pteridin-8-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   33  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   34  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   35  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   36  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+1
HETATM   37  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   38  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   54  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   55  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   56  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   57  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   58  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   59  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   60  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1   13                                                            
CONECT    2   14                                                            
CONECT    3    5   15                                                       
CONECT    4    6   15                                                       
CONECT    5    3   16                                                       
CONECT    6    4   16                                                       
CONECT    7    8   19                                                       
CONECT    8    7   21                                                       
CONECT    9   15   17                                                       
CONECT   10   18   50                                                       
CONECT   11   20   51                                                       
CONECT   12   36   37                                                       
CONECT   13    1   22   33   55                                             
CONECT   14    2   22   36   56                                             
CONECT   15    3    4    9                                                  
CONECT   16    5    6   36                                                  
CONECT   17    9   24   38   57                                             
CONECT   18   10   24   39   58                                             
CONECT   19    7   29   53   59                                             
CONECT   20   11   25   52   60                                             
CONECT   21    8   40   41                                                  
CONECT   22   13   14   37   61                                             
CONECT   23   27   28   37                                                  
CONECT   24   17   18   42   62                                             
CONECT   25   20   26   43   63                                             
CONECT   26   25   30   44   64                                             
CONECT   27   23   33   34                                                  
CONECT   28   23   35   45                                                  
CONECT   29   19   46   47                                                  
CONECT   30   26   50   52   65                                             
CONECT   31   32   34   35                                                  
CONECT   32   31                                                            
CONECT   33   13   27                                                       
CONECT   34   27   31                                                       
CONECT   35   28   31                                                       
CONECT   36   12   14   16                                                  
CONECT   37   12   22   23                                                  
CONECT   38   17                                                            
CONECT   39   18                                                            
CONECT   40   21                                                            
CONECT   41   21                                                            
CONECT   42   24                                                            
CONECT   43   25                                                            
CONECT   44   26                                                            
CONECT   45   28                                                            
CONECT   46   29                                                            
CONECT   47   29                                                            
CONECT   48   54                                                            
CONECT   49   54                                                            
CONECT   50   10   30                                                       
CONECT   51   11   54                                                       
CONECT   52   20   30                                                       
CONECT   53   19   54                                                       
CONECT   54   48   49   51   53                                             
CONECT   55   13                                                            
CONECT   56   14                                                            
CONECT   57   17                                                            
CONECT   58   18                                                            
CONECT   59   19                                                            
CONECT   60   20                                                            
CONECT   61   22                                                            
CONECT   62   24                                                            
CONECT   63   25                                                            
CONECT   64   26                                                            
CONECT   65   30                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  138    0
END

Synonyms

Value	Source
1-{4-[(6S,6ar,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-F]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-(5-O-{[(1S)-1,3-dicarboxypropoxy](hydroxy)phosphoryl}-alpha-D-ribofuranosyl)-D-ribitol	ChEBI
5,10-Methenyl-5,6,7,8-tetrahydromethanopterin	ChEBI
5,10-Methenyltetrahydromethanopterin	ChEBI
N5,N10-Methenyltetrahydromethanopterin	ChEBI
1-{4-[(6S,6ar,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-F]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-(5-O-{[(1S)-1,3-dicarboxypropoxy](hydroxy)phosphoryl}-a-D-ribofuranosyl)-D-ribitol	Generator
1-{4-[(6S,6ar,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-F]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-(5-O-{[(1S)-1,3-dicarboxypropoxy](hydroxy)phosphoryl}-α-D-ribofuranosyl)-D-ribitol	Generator

Molecular Formula

C₃₁H₄₄N₆O₁₆P

Average Mass

787.6854

Monoisotopic Mass

787.255140902

IUPAC Name

(6S,6aR,7R)-8-{4-[(2S,3S,4R)-5-{[(2S,3R,4S,5R)-5-[({[(1S)-1,3-dicarboxypropoxy](hydroxy)phosphoryl}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]oxy}-2,3,4-trihydroxypentyl]phenyl}-1-hydroxy-3-imino-6,7-dimethyl-3H,4H,5H,6H,6aH,7H-8λ⁵-imidazo[1,5-f]pteridin-8-ylium

Traditional Name

(6S,6aR,7R)-8-{4-[(2S,3S,4R)-5-{[(2S,3R,4S,5R)-5-({[(1S)-1,3-dicarboxypropoxy(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]oxy}-2,3,4-trihydroxypentyl]phenyl}-1-hydroxy-3-imino-6,7-dimethyl-4H,5H,6H,6aH,7H-8λ⁵-imidazo[1,5-f]pteridin-8-ylium

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO[C@@]1([H])O[C@]([H])(COP(O)(=O)O[C@@]([H])(CCC(O)=O)C(O)=O)[C@@]([H])(O)[C@@]1([H])O)[C@@]([H])(O)[C@@]([H])(O)CC1=CC=C(C=C1)[N+]1=CN2C3=C(NC(=N)N=C3O)N[C@@]([H])(C)[C@]2([H])[C@@]1([H])C

InChI Identifier

InChI=1S/C31H43N6O16P/c1-13-22-14(2)36(12-37(22)23-27(33-13)34-31(32)35-28(23)45)16-5-3-15(4-6-16)9-17(38)24(42)18(39)10-50-30-26(44)25(43)20(52-30)11-51-54(48,49)53-19(29(46)47)7-8-21(40)41/h3-6,12-14,17-20,22,24-26,30,38-39,42-44H,7-11H2,1-2H3,(H6-,32,33,34,35,40,41,45,46,47,48,49)/p+1/t13-,14+,17-,18+,19-,20+,22+,24-,25+,26+,30-/m0/s1

InChI Key

RANKJVUGLXUXOL-CAFBYHECSA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Fatty acyl glycoside of mono- or disaccharide
Fatty acyl glycoside
Alkyl glycoside
Pterin
O-glycosyl compound
Glycosyl compound
Pteridine
Monosaccharide phosphate
Aniline or substituted anilines
Pyrimidone
Secondary aliphatic/aromatic amine
Dialkyl phosphate
Aminopyrimidine
Alkyl phosphate
Fatty acyl
Monocyclic benzene moiety
Pyrimidine
Organic phosphoric acid derivative
Dicarboxylic acid or derivatives
Benzenoid
Phosphoric acid ester
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
2-imidazoline
Amino acid or derivatives
Amino acid
Secondary alcohol
Acetal
Amidine
Carboxylic acid amidine
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Azacycle
Organoheterocyclic compound
Secondary amine
Polyol
Organic nitrogen compound
Alcohol
Amine
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Carbonyl group
Organonitrogen compound
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

tetrahydromethanopterin (CHEBI:17975 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.14 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-7.9	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	-2.7	ChemAxon
pKa (Strongest Basic)	15	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	12	ChemAxon
Polar Surface Area	336.72 Å²	ChemAxon
Rotatable Bond Count	17	ChemAxon
Refractivity	210.59 m³·mol⁻¹	ChemAxon
Polarizability	77.16 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00yi-1708223900-723193ec2da5552ff57f	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00fr-1009300300-454925a1a40a3e7788e0	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0080-9804110000-e1c04124c92547aa6495	2019-02-22	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	783.5
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	652.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	164.6
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	392.0
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	396.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	230.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	637.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	1154.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	444.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	183.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	686.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	204.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	65.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	803.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	654.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	83.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	373.0
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	877.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	762.0

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_1	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@@H](CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)O[Si](C)(C)C)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	1994.28
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_2	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O[Si](C)(C)C)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	1633.14
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_3	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O[Si](C)(C)C)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	1861.17
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_4	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O[Si](C)(C)C)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	870.799
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_5	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O[Si](C)(C)C)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	1922.67
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_6	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O[Si](C)(C)C)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	670.043
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_7	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O[Si](C)(C)C)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	1733.92
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_8	C[C@@H]1NC2=C(C(O[Si](C)(C)C)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	1707.0
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_9	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O[C@@H](CCC(=O)O)C(=O)O)O[Si](C)(C)C)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	2153.73
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_10	C[C@@H]1NC2=C(C(O)=NC(=N)N2[Si](C)(C)C)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	1412.94
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_11	C[C@@H]1NC2=C(C(O)=NC(=N[Si](C)(C)C)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard non polar	2025-10-24	1098.77
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_12	C[C@H]1[C@@H]2[C@@H](C)[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)=CN2C2=C([NH]C(=N)N=C2O)N1[Si](C)(C)C	standard non polar	2025-10-24	3500.57
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_1	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@@H](CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)O[Si](C)(C)C)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	776.285
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_2	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O[Si](C)(C)C)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	1248.85
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_3	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O[Si](C)(C)C)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	1895.43
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_4	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O[Si](C)(C)C)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	3553.52
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_5	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O[Si](C)(C)C)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	841.932
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_6	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O[Si](C)(C)C)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	2147.09
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_7	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O[Si](C)(C)C)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	3513.19
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_8	C[C@@H]1NC2=C(C(O[Si](C)(C)C)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	2296.04
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_9	C[C@@H]1NC2=C(C(O)=NC(=N)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O[C@@H](CCC(=O)O)C(=O)O)O[Si](C)(C)C)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	3706.54
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_10	C[C@@H]1NC2=C(C(O)=NC(=N)N2[Si](C)(C)C)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	2130.71
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_11	C[C@@H]1NC2=C(C(O)=NC(=N[Si](C)(C)C)[NH]2)N2C=[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)[C@H](C)[C@@H]12	standard polar	2025-10-24	3342.01
Gas Chromatography	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin_TMS_12	C[C@H]1[C@@H]2[C@@H](C)[N+](C3=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]4O[C@H](COP(=O)(O)O[C@@H](CCC(=O)O)C(=O)O)[C@@H](O)[C@H]4O)C=C3)=CN2C2=C([NH]C(=N)N=C2O)N1[Si](C)(C)C	standard polar	2025-10-24	3650.92

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0024542	5,10-Methylenetetrahydromethanopterin	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin	F420-dependent methylenetetrahydromethanopterin dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0024543	5,10-Methylenetetrahydromethanopterin	5,10-Methenyl-5,6,7,8-tetrahydromethanopterin	F420-dependent methylenetetrahydromethanopterin dehydrogenase	Dehydrogenation	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	3	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	6		Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	16	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	22		Metabolic reconstruction
Bacteria	Proteobacteria	4	Human feces	Metabolic reconstruction
Archaea/Archaea	nah	3

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C04330

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440298

PDB ID

Not Available

ChEBI ID

17975

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 5,10-Methenyl-5,6,7,8-tetrahydromethanopterin (MMDBc0048048)

MOL for #<Metabolite:0x00007f9a903e19a8>

3D MOL for #<Metabolite:0x00007f9a903e19a8>

3D SDF for #<Metabolite:0x00007f9a903e19a8>

3D-SDF for #<Metabolite:0x00007f9a903e19a8>

PDB for #<Metabolite:0x00007f9a903e19a8>

3D PDB for #<Metabolite:0x00007f9a903e19a8>

SMILES for #<Metabolite:0x00007f9a903e19a8>

INCHI for #<Metabolite:0x00007f9a903e19a8>

Structure for #<Metabolite:0x00007f9a903e19a8>

3D Structure for #<Metabolite:0x00007f9a903e19a8>