MiMeDB: Showing metabocard for Cyclo(D-Arg-L-Pro) (MMDBc0015705)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:29:41 UTC

Update Date

2025-10-07 16:06:27 UTC

Metabolite ID

MMDBc0015705

Metabolite Identification

Common Name

Cyclo(D-Arg-L-Pro)

Description

Cyclo(D-Arg-L-Pro) is a cyclic dipeptide, a class of compounds formed by the condensation of two amino acids. There is limited literature available on this metabolite, indicating that its biological significance and potential applications remain largely unexplored.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152108292D          

 20 21  0  0  1  0            999 V2000
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1354    2.1307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4710    1.3770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3149    2.0445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -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    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6116    0.4894    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  6  0  0  0
  8  4  1  0  0  0  0
  9  8  1  0  0  0  0
 10  7  1  0  0  0  0
 12 11  2  0  0  0  0
 13 11  1  0  0  0  0
 14  5  1  0  0  0  0
 14 11  1  0  0  0  0
 15  7  1  0  0  0  0
 15  9  2  0  0  0  0
 16  6  1  0  0  0  0
 16  8  1  0  0  0  0
 16 10  1  0  0  0  0
 17  9  1  0  0  0  0
 18 10  2  0  0  0  0
  7 19  1  1  0  0  0
  8 20  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0015705

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12CCCN1C(=O)[C@]([H])(CCCNC(N)=N)N=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C11H19N5O2/c12-11(13)14-5-1-3-7-10(18)16-6-2-4-8(16)9(17)15-7/h7-8H,1-6H2,(H,15,17)(H4,12,13,14)/t7-,8+/m0/s1

> <INCHI_KEY>
ZRJHYOXNWCMGMW-JGVFFNPUSA-N

> <FORMULA>
C11H19N5O2

> <MOLECULAR_WEIGHT>
253.306

> <EXACT_MASS>
253.153874872

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
26.749808333489

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-{3-[(3S,8aR)-1-hydroxy-4-oxo-3H,4H,6H,7H,8H,8aH-pyrrolo[1,2-a]pyrazin-3-yl]propyl}guanidine

> <ALOGPS_LOGP>
-0.92

> <JCHEM_LOGP>
-2.5361258017380393

> <ALOGPS_LOGS>
-2.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
19.43446677771816

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.643085514758579

> <JCHEM_PKA_STRONGEST_BASIC>
12.118457009007608

> <JCHEM_POLAR_SURFACE_AREA>
114.80000000000001

> <JCHEM_REFRACTIVITY>
76.2314

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.81e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-{3-[(3S,8aR)-1-hydroxy-4-oxo-3H,6H,7H,8H,8aH-pyrrolo[1,2-a]pyrazin-3-yl]propyl}guanidine

> <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      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.853   3.977   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.479   2.570   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.321   3.816   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       5.335   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       4.001  -2.310   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0      -4.001  -0.770   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -4.001   2.310   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      -6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      -6.742   0.914   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    1   14                                                       
CONECT    6    2   16                                                       
CONECT    7    3   10   15   19                                             
CONECT    8    4    9   16   20                                             
CONECT    9    8   15   17                                                  
CONECT   10    7   16   18                                                  
CONECT   11   12   13   14                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    5   11                                                       
CONECT   15    7    9                                                       
CONECT   16    6    8   10                                                  
CONECT   17    9                                                            
CONECT   18   10                                                            
CONECT   19    7                                                            
CONECT   20    8                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₁₉N₅O₂

Average Mass

253.306

Monoisotopic Mass

253.153874872

IUPAC Name

N-{3-[(3S,8aR)-1-hydroxy-4-oxo-3H,4H,6H,7H,8H,8aH-pyrrolo[1,2-a]pyrazin-3-yl]propyl}guanidine

Traditional Name

N-{3-[(3S,8aR)-1-hydroxy-4-oxo-3H,6H,7H,8H,8aH-pyrrolo[1,2-a]pyrazin-3-yl]propyl}guanidine

CAS Registry Number

Not Available

SMILES

[H][C@]12CCCN1C(=O)[C@]([H])(CCCNC(N)=N)N=C2O

InChI Identifier

InChI=1S/C11H19N5O2/c12-11(13)14-5-1-3-7-10(18)16-6-2-4-8(16)9(17)15-7/h7-8H,1-6H2,(H,15,17)(H4,12,13,14)/t7-,8+/m0/s1

InChI Key

ZRJHYOXNWCMGMW-JGVFFNPUSA-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
N-alkylpiperazine
1,4-diazinane
Piperazine
Pyrrolidine
Tertiary carboxylic acid amide
Carboxamide group
Guanidine
Lactam
Secondary carboxylic acid amide
Azacycle
Organoheterocyclic compound
Carboximidamide
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organic nitrogen compound
Organic oxide
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.88 g/L	ALOGPS
logP	-0.92	ALOGPS
logP	-2.5	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	4.64	ChemAxon
pKa (Strongest Basic)	12.12	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	114.8 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	76.23 m³·mol⁻¹	ChemAxon
Polarizability	26.75 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

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	Proteobacteria	1	Human feces; Human ; Human sputum; Human urine; Human supragingival plaque; Human saliva; Human mucosa	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	1	Human feces; Human ; Human sputum; Human urine; Human supragingival plaque; Human saliva; Human mucosa	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

4450341

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5288107

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 Cyclo(D-Arg-L-Pro) (MMDBc0015705)

MOL for #<Metabolite:0x00007f8d91c532c8>

3D MOL for #<Metabolite:0x00007f8d91c532c8>

3D SDF for #<Metabolite:0x00007f8d91c532c8>

3D-SDF for #<Metabolite:0x00007f8d91c532c8>

PDB for #<Metabolite:0x00007f8d91c532c8>

3D PDB for #<Metabolite:0x00007f8d91c532c8>

SMILES for #<Metabolite:0x00007f8d91c532c8>

INCHI for #<Metabolite:0x00007f8d91c532c8>

Structure for #<Metabolite:0x00007f8d91c532c8>

3D Structure for #<Metabolite:0x00007f8d91c532c8>