MiMeDB: Showing metabocard for Nitracidomycin A (MMDBc0020749)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 10:54:05 UTC

Update Date

2022-08-31 06:47:07 UTC

Metabolite ID

MMDBc0020749

Metabolite Identification

Common Name

Nitracidomycin A

Description

Nitracidomycin A belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom. Nitracidomycin A is a moderately basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152112542D          

 23 22  0  0  1  0            999 V2000
    1.6500   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -2.1434    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -2.8579    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  6  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  1  0  0  0  0
 10  9  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  2  0  0  0  0
  9 12  1  6  0  0  0
 13  5  2  0  0  0  0
  8 14  1  4  0  0  0
 10 15  1  1  0  0  0
 16 11  2  0  0  0  0
 17 11  1  0  0  0  0
 18 13  2  0  0  0  0
 19  4  1  0  0  0  0
 19 13  1  0  0  0  0
 20  5  1  0  0  0  0
  7 21  1  1  0  0  0
  9 22  1  1  0  0  0
 10 23  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0020749

> <DATABASE_NAME>
MIME

> <SMILES>
[H]C(C(O)=N[C@]([H])(C(C)C)[C@]([H])(O)[C@]([H])(C)C(O)=O)=N(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C11H20N2O6/c1-6(2)9(10(15)7(3)11(16)17)12-8(14)5-13(18)19-4/h5-7,9-10,15H,1-4H3,(H,12,14)(H,16,17)/b13-5+/t7-,9+,10+/m0/s1

> <INCHI_KEY>
GMJHMZVGDYXZRQ-TYDGNEIFSA-N

> <FORMULA>
C11H20N2O6

> <MOLECULAR_WEIGHT>
276.289

> <EXACT_MASS>
276.132136372

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
26.842307579335078

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-{[(1S,2R,3R)-1-carboxy-2-hydroxy-1,4-dimethylpentan-3-yl]-C-hydroxycarbonimidoyl}-N-methoxymethanimine oxide

> <ALOGPS_LOGP>
-0.11

> <JCHEM_LOGP>
0.9353399345476551

> <ALOGPS_LOGS>
-2.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.159194177588327

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.260456894250885

> <JCHEM_PKA_STRONGEST_BASIC>
1.3841223461588568

> <JCHEM_POLAR_SURFACE_AREA>
128.1

> <JCHEM_REFRACTIVITY>
75.6378

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.34e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-{[(1S,2R,3R)-1-carboxy-2-hydroxy-1,4-dimethylpentan-3-yl]-C-hydroxycarbonimidoyl}-N-methoxymethanimine oxide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0       3.080  -0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.390   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.930   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.540  -5.335   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.310  -4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.620   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.700   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.390  -1.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.930  -1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.240   0.000   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       4.620  -2.667   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.770  -4.001   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.700  -2.667   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      10.010   1.334   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      10.010  -1.334   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000  -2.667   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000  -5.335   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0       3.080  -5.335   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       6.160   0.000   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       6.160  -2.667   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       8.470  -1.334   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2    6                                                            
CONECT    3    7                                                            
CONECT    4   19                                                            
CONECT    5    8   13   20                                                  
CONECT    6    1    2    9                                                  
CONECT    7    3   10   11   21                                             
CONECT    8    5   12   14                                                  
CONECT    9    6   10   12   22                                             
CONECT   10    7    9   15   23                                             
CONECT   11    7   16   17                                                  
CONECT   12    8    9                                                       
CONECT   13    5   18   19                                                  
CONECT   14    8                                                            
CONECT   15   10                                                            
CONECT   16   11                                                            
CONECT   17   11                                                            
CONECT   18   13                                                            
CONECT   19    4   13                                                       
CONECT   20    5                                                            
CONECT   21    7                                                            
CONECT   22    9                                                            
CONECT   23   10                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   44    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₂₀N₂O₆

Average Mass

276.289

Monoisotopic Mass

276.132136372

IUPAC Name

1-{[(1S,2R,3R)-1-carboxy-2-hydroxy-1,4-dimethylpentan-3-yl]-C-hydroxycarbonimidoyl}-N-methoxymethanimine oxide

Traditional Name

1-{[(1S,2R,3R)-1-carboxy-2-hydroxy-1,4-dimethylpentan-3-yl]-C-hydroxycarbonimidoyl}-N-methoxymethanimine oxide

CAS Registry Number

Not Available

SMILES

[H]C(C(O)=N[C@]([H])(C(C)C)[C@]([H])(O)[C@]([H])(C)C(O)=O)=N(=O)OC

InChI Identifier

InChI=1S/C11H20N2O6/c1-6(2)9(10(15)7(3)11(16)17)12-8(14)5-13(18)19-4/h5-7,9-10,15H,1-4H3,(H,12,14)(H,16,17)/b13-5+/t7-,9+,10+/m0/s1

InChI Key

GMJHMZVGDYXZRQ-TYDGNEIFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma 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

Gamma amino acids and derivatives

Alternative Parents

Substituents

Gamma amino acid or derivatives
Medium-chain hydroxy acid
Medium-chain fatty acid
Methyl-branched fatty acid
Hydroxy fatty acid
Branched fatty acid
Beta-hydroxy acid
Amino fatty acid
Fatty acyl
Fatty acid
Hydroxy acid
Secondary alcohol
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Allyl-type 1,3-dipolar organic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic zwitterion
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.93 g/L	ALOGPS
logP	-0.11	ALOGPS
logP	0.94	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	3.26	ChemAxon
pKa (Strongest Basic)	1.38	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	128.1 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	75.64 m³·mol⁻¹	ChemAxon
Polarizability	26.84 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

Not Available

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	Actinobacteria	2		Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

78442962

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139588955

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Nitracidomycin A (MMDBc0020749)

MOL for #<Metabolite:0x00007fed159614f0>

3D MOL for #<Metabolite:0x00007fed159614f0>

3D SDF for #<Metabolite:0x00007fed159614f0>

3D-SDF for #<Metabolite:0x00007fed159614f0>

PDB for #<Metabolite:0x00007fed159614f0>

3D PDB for #<Metabolite:0x00007fed159614f0>

SMILES for #<Metabolite:0x00007fed159614f0>

INCHI for #<Metabolite:0x00007fed159614f0>

Structure for #<Metabolite:0x00007fed159614f0>

3D Structure for #<Metabolite:0x00007fed159614f0>