MiMeDB: Showing metabocard for 7-Aminomethyl-7-deazaguanosine (MMDBc0031795)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:49:36 UTC

Update Date

2022-08-31 18:24:47 UTC

Metabolite ID

MMDBc0031795

Metabolite Identification

Common Name

7-Aminomethyl-7-deazaguanosine

Description

7-Aminomethyl-7-deazaguanosine is an intermediate in tRNA charging and tRNA queosine synthesis. It is a substrate for S-adenosylmethionine:tRNA ribosyltransferase-isomerase which catalyzes the reaction: S-adenosylmethionine + 7-aminomethyl-7-deazaguanosine = methionine + adenine + epoxyqueuosine

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10101211222D          

 26 28  0  0  0  0            999 V2000
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -3.2299    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0865   -2.8174    0.0000 C   0  0  2  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
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1536    1.3672    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7643   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -4.2695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9115   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -2.4049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7831   -3.9515    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7471   -4.2326    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4610   -3.5525    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4164   -2.0209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  1  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 13  1  1  0  0  0  0
 14 12  2  0  0  0  0
 15  9  1  0  0  0  0
 15 12  1  0  0  0  0
 16 10  2  0  0  0  0
 16 12  1  0  0  0  0
 17  2  1  0  0  0  0
 17  9  1  0  0  0  0
 11 17  1  1  0  0  0
 18  3  1  0  0  0  0
  7 19  1  6  0  0  0
  8 20  1  6  0  0  0
 21 10  1  0  0  0  0
 22  5  1  0  0  0  0
 22 11  1  0  0  0  0
  5 23  1  6  0  0  0
  7 24  1  1  0  0  0
  8 25  1  1  0  0  0
 11 26  1  6  0  0  0
M  END


  Mrv0541 10101211222D          

 26 28  0  0  0  0            999 V2000
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -3.2299    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0865   -2.8174    0.0000 C   0  0  2  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
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1536    1.3672    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7643   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -4.2695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9115   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -2.4049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7831   -3.9515    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7471   -4.2326    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4610   -3.5525    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4164   -2.0209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  1  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 13  1  1  0  0  0  0
 14 12  2  0  0  0  0
 15  9  1  0  0  0  0
 15 12  1  0  0  0  0
 16 10  2  0  0  0  0
 16 12  1  0  0  0  0
 17  2  1  0  0  0  0
 17  9  1  0  0  0  0
 11 17  1  1  0  0  0
 18  3  1  0  0  0  0
  7 19  1  6  0  0  0
  8 20  1  6  0  0  0
 21 10  1  0  0  0  0
 22  5  1  0  0  0  0
 22 11  1  0  0  0  0
  5 23  1  6  0  0  0
  7 24  1  1  0  0  0
  8 25  1  1  0  0  0
 11 26  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031795

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=C(CN)C3=C2NC(=N)N=C3O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C12H17N5O5/c13-1-4-2-17(9-6(4)10(21)16-12(14)15-9)11-8(20)7(19)5(3-18)22-11/h2,5,7-8,11,18-20H,1,3,13H2,(H3,14,15,16,21)/t5-,7-,8-,11-/m1/s1

> <INCHI_KEY>
SOEYIPCQNRSIAV-IOSLPCCCSA-N

> <FORMULA>
C12H17N5O5

> <MOLECULAR_WEIGHT>
311.2939

> <EXACT_MASS>
311.122968679

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
30.14154001179891

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-2-[5-(aminomethyl)-4-hydroxy-2-imino-1H,2H,7H-pyrrolo[2,3-d]pyrimidin-7-yl]-5-(hydroxymethyl)oxolane-3,4-diol

> <ALOGPS_LOGP>
-1.78

> <JCHEM_LOGP>
-3.133205254793236

> <ALOGPS_LOGS>
-1.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.457371601038751

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.424319473557948

> <JCHEM_PKA_STRONGEST_BASIC>
9.088894052933215

> <JCHEM_POLAR_SURFACE_AREA>
169.33999999999997

> <JCHEM_REFRACTIVITY>
85.85159999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.19e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5R)-2-[5-(aminomethyl)-4-hydroxy-2-imino-1H-pyrrolo[2,3-d]pyrimidin-7-yl]-5-(hydroxymethyl)oxolane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-12         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  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    4   13                                                       
CONECT    2    4   17                                                       
CONECT    3    5   18                                                       
CONECT    4    1    2    6                                                  
CONECT    5    3    7   22   23                                             
CONECT    6    4    9   10                                                  
CONECT    7    5    8   19   24                                             
CONECT    8    7   11   20   25                                             
CONECT    9    6   15   17                                                  
CONECT   10    6   16   21                                                  
CONECT   11    8   17   22   26                                             
CONECT   12   14   15   16                                                  
CONECT   13    1                                                            
CONECT   14   12                                                            
CONECT   15    9   12                                                       
CONECT   16   10   12                                                       
CONECT   17    2    9   11                                                  
CONECT   18    3                                                            
CONECT   19    7                                                            
CONECT   20    8                                                            
CONECT   21   10                                                            
CONECT   22    5   11                                                       
CONECT   23    5                                                            
CONECT   24    7                                                            
CONECT   25    8                                                            
CONECT   26   11                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

Synonyms

Not Available

Molecular Formula

C₁₂H₁₇N₅O₅

Average Mass

311.2939

Monoisotopic Mass

311.122968679

IUPAC Name

(2R,3R,4S,5R)-2-[5-(aminomethyl)-4-hydroxy-2-imino-1H,2H,7H-pyrrolo[2,3-d]pyrimidin-7-yl]-5-(hydroxymethyl)oxolane-3,4-diol

Traditional Name

(2R,3R,4S,5R)-2-[5-(aminomethyl)-4-hydroxy-2-imino-1H-pyrrolo[2,3-d]pyrimidin-7-yl]-5-(hydroxymethyl)oxolane-3,4-diol

CAS Registry Number

Not Available

SMILES

[H][C@]1(CO)O[C@@]([H])(N2C=C(CN)C3=C2NC(=N)N=C3O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C12H17N5O5/c13-1-4-2-17(9-6(4)10(21)16-12(14)15-9)11-8(20)7(19)5(3-18)22-11/h2,5,7-8,11,18-20H,1,3,13H2,(H3,14,15,16,21)/t5-,7-,8-,11-/m1/s1

InChI Key

SOEYIPCQNRSIAV-IOSLPCCCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolopyrimidine nucleosides and nucleotides. These are nucleoside derivatives containing a ribose derivative which is n-glycosylated to a pyrrolopyrimidine. Also called deazapurine nucleosides, they are analogs of purine nucleosides with the N atom of the purine being replaced by a C atom at position 7.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrrolopyrimidine nucleosides and nucleotides

Sub Class

Not Available

Direct Parent

Pyrrolopyrimidine nucleosides and nucleotides

Alternative Parents

Substituents

Pyrrolopyrimidine ribonucleoside
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
Pyrrolo[2,3-d]pyrimidine
Pyrrolopyrimidine
Aralkylamine
Pyrimidone
Aminopyrimidine
Substituted pyrrole
Pyrimidine
Monosaccharide
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Pyrrole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Amine
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	8.19 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-3.1	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	7.42	ChemAxon
pKa (Strongest Basic)	9.09	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	169.34 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	85.85 m³·mol⁻¹	ChemAxon
Polarizability	30.14 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

191792

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Sajed T, Marcu A, Ramirez M, Pon A, Guo AC, Knox C, Wilson M, Grant JR, Djoumbou Y, Wishart DS: ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. Nucleic Acids Res. 2016 Jan 4;44(D1):D495-501. doi: 10.1093/nar/gkv1060. Epub 2015 Oct 19. [PubMed:26481353 ]

Showing metabocard for 7-Aminomethyl-7-deazaguanosine (MMDBc0031795)

MOL for #<Metabolite:0x00007f92501db638>

3D MOL for #<Metabolite:0x00007f92501db638>

3D SDF for #<Metabolite:0x00007f92501db638>

3D-SDF for #<Metabolite:0x00007f92501db638>

PDB for #<Metabolite:0x00007f92501db638>

3D PDB for #<Metabolite:0x00007f92501db638>

SMILES for #<Metabolite:0x00007f92501db638>

INCHI for #<Metabolite:0x00007f92501db638>

Structure for #<Metabolite:0x00007f92501db638>

3D Structure for #<Metabolite:0x00007f92501db638>