MiMeDB: Showing metabocard for 5S-hydroxynorvaline-S-Ile (MMDBc0028060)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 17:41:09 UTC

Update Date

2025-10-07 16:07:48 UTC

Metabolite ID

MMDBc0028060

Metabolite Identification

Common Name

5S-hydroxynorvaline-S-Ile

Description

5S-hydroxynorvaline-S-Ile is a diketopiperazine alkaloid, a chemical class characterized by a cyclic structure formed from two amino acids linked by peptide bonds. Its chemical structure features a hydroxyl group at the 5th position of the norvaline moiety, which contributes to its unique properties. This compound has been isolated from the Chinese mangrove endophytic fungus Penicillium sp., alongside other metabolites, suggesting a diverse biosynthetic capability within this organism (PMID:29860997 ). In terms of biological pathways, diketopiperazines like 5S-hydroxynorvaline-S-Ile are often involved in various metabolic processes, including those related to secondary metabolite production, which can play roles in ecological interactions and potential pharmacological activities. The specific pathways of 5S-hydroxynorvaline-S-Ile are not extensively detailed in literature, but diketopiperazines generally contribute to the biosynthesis of bioactive compounds, potentially influencing microbial interactions and plant defense mechanisms.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152119412D          

 19 19  0  0  1  0            999 V2000
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  7  2  1  1  0  0  0
  7  3  1  0  0  0  0
  8  5  1  6  0  0  0
  9  7  1  6  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  8  1  0  0  0  0
 12 11  2  0  0  0  0
 13  9  1  0  0  0  0
 13 10  2  0  0  0  0
 14  6  1  0  0  0  0
 15 10  1  0  0  0  0
 16 11  1  0  0  0  0
  7 17  1  6  0  0  0
  8 18  1  1  0  0  0
  9 19  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0028060

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](C)(CC)[C@]1([H])N=C(O)[C@]([H])(CCCO)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C11H20N2O3/c1-3-7(2)9-11(16)12-8(5-4-6-14)10(15)13-9/h7-9,14H,3-6H2,1-2H3,(H,12,16)(H,13,15)/t7-,8-,9-/m0/s1

> <INCHI_KEY>
PWIAWDVLQXARBI-CIUDSAMLSA-N

> <FORMULA>
C11H20N2O3

> <MOLECULAR_WEIGHT>
228.292

> <EXACT_MASS>
228.147392512

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
24.706741102130707

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,6S)-3-[(2S)-butan-2-yl]-6-(3-hydroxypropyl)-3,6-dihydropyrazine-2,5-diol

> <ALOGPS_LOGP>
0.72

> <JCHEM_LOGP>
-0.27411798918526553

> <ALOGPS_LOGS>
-2.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.6862658042386434

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.398683706587466

> <JCHEM_PKA_STRONGEST_BASIC>
5.594028863455469

> <JCHEM_POLAR_SURFACE_AREA>
85.41000000000001

> <JCHEM_REFRACTIVITY>
60.288500000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.70e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S)-3-[(2S)-butan-2-yl]-6-(3-hydroxypropyl)-3,6-dihydropyrazine-2,5-diol

> <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       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       1.334   5.390   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       2.667  -1.540   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       2.667   3.080   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    7                                                            
CONECT    3    1    7                                                       
CONECT    4    5    6                                                       
CONECT    5    4    8                                                       
CONECT    6    4   14                                                       
CONECT    7    2    3    9   17                                             
CONECT    8    5   10   12   18                                             
CONECT    9    7   11   13   19                                             
CONECT   10    8   13   15                                                  
CONECT   11    9   12   16                                                  
CONECT   12    8   11                                                       
CONECT   13    9   10                                                       
CONECT   14    6                                                            
CONECT   15   10                                                            
CONECT   16   11                                                            
CONECT   17    7                                                            
CONECT   18    8                                                            
CONECT   19    9                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₂₀N₂O₃

Average Mass

228.292

Monoisotopic Mass

228.147392512

IUPAC Name

(3S,6S)-3-[(2S)-butan-2-yl]-6-(3-hydroxypropyl)-3,6-dihydropyrazine-2,5-diol

Traditional Name

(3S,6S)-3-[(2S)-butan-2-yl]-6-(3-hydroxypropyl)-3,6-dihydropyrazine-2,5-diol

CAS Registry Number

Not Available

SMILES

[H][C@](C)(CC)[C@]1([H])N=C(O)[C@]([H])(CCCO)N=C1O

InChI Identifier

InChI=1S/C11H20N2O3/c1-3-7(2)9-11(16)12-8(5-4-6-14)10(15)13-9/h7-9,14H,3-6H2,1-2H3,(H,12,16)(H,13,15)/t7-,8-,9-/m0/s1

InChI Key

PWIAWDVLQXARBI-CIUDSAMLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic carboximidic acids. These are organic acids with the general formula RC(=N)-OH (R=H, organic group), where the carboximidic acid group is part of a cycle.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboximidic acids and derivatives

Sub Class

Carboximidic acids

Direct Parent

Cyclic carboximidic acids

Alternative Parents

Substituents

Cyclic carboximidic acid
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.77 g/L	ALOGPS
logP	0.72	ALOGPS
logP	-0.27	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	-0.4	ChemAxon
pKa (Strongest Basic)	5.59	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	85.41 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	60.29 m³·mol⁻¹	ChemAxon
Polarizability	24.71 Å³	ChemAxon
Number of Rings	1	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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

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

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
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

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

71048453

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

146684494

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 5S-hydroxynorvaline-S-Ile (MMDBc0028060)

MOL for #<Metabolite:0x00007fae012b2030>

3D MOL for #<Metabolite:0x00007fae012b2030>

3D SDF for #<Metabolite:0x00007fae012b2030>

3D-SDF for #<Metabolite:0x00007fae012b2030>

PDB for #<Metabolite:0x00007fae012b2030>

3D PDB for #<Metabolite:0x00007fae012b2030>

SMILES for #<Metabolite:0x00007fae012b2030>

INCHI for #<Metabolite:0x00007fae012b2030>

Structure for #<Metabolite:0x00007fae012b2030>

3D Structure for #<Metabolite:0x00007fae012b2030>