MiMeDB: Showing metabocard for Cis-cyclo-(His,Leu) (MMDBc0018650)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:49:03 UTC

Update Date

2025-10-07 16:06:52 UTC

Metabolite ID

MMDBc0018650

Metabolite Identification

Common Name

Cis-cyclo-(His,Leu)

Description

Cis-cyclo-(His,Leu) is a diketopiperazine, a class of cyclic dipeptides characterized by their unique ring structure formed by the condensation of two amino acids. Specifically, cis-cyclo-(His,Leu) consists of histidine and leucine, linked in a cyclic arrangement that influences its chemical properties and biological activities. The compound has been isolated from the ethyl acetate extract of a strain of Bacillus spp., highlighting its potential as a bioactive secondary metabolite (PMID:22335791 ). Diketopiperazines like cis-cyclo-(His,Leu) are known to participate in various biochemical pathways, including those involved in microbial interactions and signaling processes. They may play roles in the regulation of cellular functions, influencing growth and development in microbial communities. Additionally, the structural features of cis-cyclo-(His,Leu) suggest potential interactions with biological targets, which could lead to further exploration of its pharmacological applications. The study of such metabolites contributes to our understanding of microbial ecology and the development of novel therapeutic agents derived from natural products.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152110492D          

 20 21  0  0  1  0            999 V2000
    5.7158    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.2911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8109    2.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309    2.1965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    6.7661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.4661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    5.5286    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    4.7036    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    4.2911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5559    2.1965    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4760    2.9812    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    4.7036    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    5.5286    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    6.7661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    3.4661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    6.3536    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    5.1161    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  0  0  0  0
  7  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  8  5  2  0  0  0  0
  9  3  1  6  0  0  0
 10  4  1  6  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13  5  1  0  0  0  0
 13  6  2  0  0  0  0
 14  6  1  0  0  0  0
 14  8  1  0  0  0  0
 15  9  1  0  0  0  0
 15 12  2  0  0  0  0
 16 10  1  0  0  0  0
 16 11  2  0  0  0  0
 17 11  1  0  0  0  0
 18 12  1  0  0  0  0
  9 19  1  1  0  0  0
 10 20  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0018650

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(CC(C)C)N=C(O)[C@]([H])(CC2=CN=CN2)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C12H18N4O2/c1-7(2)3-9-11(17)16-10(12(18)15-9)4-8-5-13-6-14-8/h5-7,9-10H,3-4H2,1-2H3,(H,13,14)(H,15,18)(H,16,17)/t9-,10-/m0/s1

> <INCHI_KEY>
QYFSHTYKVAOVJM-UWVGGRQHSA-N

> <FORMULA>
C12H18N4O2

> <MOLECULAR_WEIGHT>
250.302

> <EXACT_MASS>
250.142975836

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
26.336211413877983

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S)-3-[(1H-imidazol-5-yl)methyl]-6-(2-methylpropyl)-3,6-dihydropyrazine-2,5-diol

> <ALOGPS_LOGP>
0.49

> <JCHEM_LOGP>
-0.7491125110942202

> <ALOGPS_LOGS>
-2.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
4.351287824320668

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.7979665917775227

> <JCHEM_PKA_STRONGEST_BASIC>
6.771929774193916

> <JCHEM_POLAR_SURFACE_AREA>
93.86

> <JCHEM_REFRACTIVITY>
66.8735

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.65e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S)-3-(3H-imidazol-4-ylmethyl)-6-(2-methylpropyl)-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      10.669  13.400   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002  13.400   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336  11.090   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   8.010   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.247   5.565   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.231   4.100   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.336  12.630   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001   6.470   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.002  10.320   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335   8.780   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668  11.090   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.668   8.010   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.771   4.100   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.755   5.565   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       8.002   8.780   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       5.335  10.320   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0       6.668  12.630   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.668   6.470   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       8.002  11.860   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       4.001   9.550   0.000  0.00  0.00           H+0
CONECT    1    7                                                            
CONECT    2    7                                                            
CONECT    3    7    9                                                       
CONECT    4    8   10                                                       
CONECT    5    8   13                                                       
CONECT    6   13   14                                                       
CONECT    7    1    2    3                                                  
CONECT    8    4    5   14                                                  
CONECT    9    3   11   15   19                                             
CONECT   10    4   12   16   20                                             
CONECT   11    9   16   17                                                  
CONECT   12   10   15   18                                                  
CONECT   13    5    6                                                       
CONECT   14    6    8                                                       
CONECT   15    9   12                                                       
CONECT   16   10   11                                                       
CONECT   17   11                                                            
CONECT   18   12                                                            
CONECT   19    9                                                            
CONECT   20   10                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

Synonyms

Value	Source
Cyclo(his-leu)	MeSH
Cyclo(L-his-L-leu)	MeSH

Molecular Formula

C₁₂H₁₈N₄O₂

Average Mass

250.302

Monoisotopic Mass

250.142975836

IUPAC Name

(3S,6S)-3-[(1H-imidazol-5-yl)methyl]-6-(2-methylpropyl)-3,6-dihydropyrazine-2,5-diol

Traditional Name

(3S,6S)-3-(3H-imidazol-4-ylmethyl)-6-(2-methylpropyl)-3,6-dihydropyrazine-2,5-diol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC(C)C)N=C(O)[C@]([H])(CC2=CN=CN2)N=C1O

InChI Identifier

InChI=1S/C12H18N4O2/c1-7(2)3-9-11(17)16-10(12(18)15-9)4-8-5-13-6-14-8/h5-7,9-10H,3-4H2,1-2H3,(H,13,14)(H,15,18)(H,16,17)/t9-,10-/m0/s1

InChI Key

QYFSHTYKVAOVJM-UWVGGRQHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Dioxopiperazine
2,5-dioxopiperazine
1,4-diazinane
Piperazine
Azole
Heteroaromatic compound
Imidazole
Carboxamide group
Secondary carboxylic acid amide
Lactam
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.36 g/L	ALOGPS
logP	0.49	ALOGPS
logP	-0.75	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	-0.8	ChemAxon
pKa (Strongest Basic)	6.77	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	93.86 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	66.87 m³·mol⁻¹	ChemAxon
Polarizability	26.34 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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)	2025-10-23	234.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	179.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	258.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	289.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	297.2
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	215.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	676.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	192.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	309.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	153.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	321.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	154.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	90.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	97.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	303.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	61.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	192.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	920.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	631.7

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_1	CC(C)C[C@@H]1N=C(O[Si](C)(C)C)[C@H](CC2=CN=C[NH]2)N=C1O	standard non polar	2025-10-23	1648.67
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_2	CC(C)C[C@@H]1N=C(O)[C@H](CC2=CN=C[NH]2)N=C1O[Si](C)(C)C	standard non polar	2025-10-23	1763.08
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_3	CC(C)C[C@@H]1N=C(O)[C@H](CC2=CN=CN2[Si](C)(C)C)N=C1O	standard non polar	2025-10-23	2234.47
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_4	CC(C)C[C@@H]1N=C(O[Si](C)(C)C)[C@H](CC2=CN=C[NH]2)N=C1O[Si](C)(C)C	standard non polar	2025-10-23	2375.42
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_5	CC(C)C[C@@H]1N=C(O[Si](C)(C)C)[C@H](CC2=CN=CN2[Si](C)(C)C)N=C1O	standard non polar	2025-10-23	2303.59
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_6	CC(C)C[C@@H]1N=C(O)[C@H](CC2=CN=CN2[Si](C)(C)C)N=C1O[Si](C)(C)C	standard non polar	2025-10-23	2668.84
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_7	CC(C)C[C@@H]1N=C(O[Si](C)(C)C)[C@H](CC2=CN=CN2[Si](C)(C)C)N=C1O[Si](C)(C)C	standard non polar	2025-10-23	1322.57
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_1	CC(C)C[C@@H]1N=C(O[Si](C)(C)C)[C@H](CC2=CN=C[NH]2)N=C1O	standard polar	2025-10-23	1882.42
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_2	CC(C)C[C@@H]1N=C(O)[C@H](CC2=CN=C[NH]2)N=C1O[Si](C)(C)C	standard polar	2025-10-23	1783.01
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_3	CC(C)C[C@@H]1N=C(O)[C@H](CC2=CN=CN2[Si](C)(C)C)N=C1O	standard polar	2025-10-23	2171.04
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_4	CC(C)C[C@@H]1N=C(O[Si](C)(C)C)[C@H](CC2=CN=C[NH]2)N=C1O[Si](C)(C)C	standard polar	2025-10-23	3124.44
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_5	CC(C)C[C@@H]1N=C(O[Si](C)(C)C)[C@H](CC2=CN=CN2[Si](C)(C)C)N=C1O	standard polar	2025-10-23	2060.74
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_6	CC(C)C[C@@H]1N=C(O)[C@H](CC2=CN=CN2[Si](C)(C)C)N=C1O[Si](C)(C)C	standard polar	2025-10-23	2905.4
Gas Chromatography	Cis-cyclo-(His,Leu)_TMS_7	CC(C)C[C@@H]1N=C(O[Si](C)(C)C)[C@H](CC2=CN=CN2[Si](C)(C)C)N=C1O[Si](C)(C)C	standard polar	2025-10-23	1243.49

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
Bacteria/Eubacteria	Firmicutes	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Firmicutes	1	Human ; 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

4955548

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6453155

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 Cis-cyclo-(His,Leu) (MMDBc0018650)

MOL for #<Metabolite:0x00007f9aa3311380>

3D MOL for #<Metabolite:0x00007f9aa3311380>

3D SDF for #<Metabolite:0x00007f9aa3311380>

3D-SDF for #<Metabolite:0x00007f9aa3311380>

PDB for #<Metabolite:0x00007f9aa3311380>

3D PDB for #<Metabolite:0x00007f9aa3311380>

SMILES for #<Metabolite:0x00007f9aa3311380>

INCHI for #<Metabolite:0x00007f9aa3311380>

Structure for #<Metabolite:0x00007f9aa3311380>

3D Structure for #<Metabolite:0x00007f9aa3311380>