MiMeDB: Showing metabocard for hydrogenobyrinate a,c-diamide (MMDBc0056031)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:13:47 UTC

Update Date

2022-08-12 20:09:32 UTC

Metabolite ID

MMDBc0056031

Metabolite Identification

Common Name

hydrogenobyrinate a,c-diamide

Description

Based on a literature review very few articles have been published on 2-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-3-(carboximidatomethyl)-4,9,14,18-tetrakis(2-carboxyethyl)-19-(carboxymethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-8-yl]ethanecarboximidate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222132D          

 69 73  0  0  1  0            999 V2000
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M  CHG  2  52  -1  53  -1
M  END


  Mrv1652306172222132D          

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 64 18  1  0  0  0  0
 23 65  1  1  0  0  0
 24 66  1  6  0  0  0
 25 67  1  1  0  0  0
 26 68  1  6  0  0  0
 40 69  1  1  0  0  0
M  CHG  2  52  -1  53  -1
M  END
> <DATABASE_ID>
MMDBc0056031

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C1=C2\N=C(\C(\C)=C3/N[C@@](C)([C@]4([H])N=C(\C(C)=C5\N=C1C(C)(C)[C@]5([H])CCC(O)=O)[C@](C)(CCC(O)=O)[C@@]4([H])CC(O)=O)[C@@](C)(CC([O-])=N)[C@]3([H])CCC(O)=O)[C@@](C)(CC([O-])=N)[C@]2([H])CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C45H62N6O12/c1-21-36-24(10-13-32(56)57)41(3,4)28(49-36)18-27-23(9-12-31(54)55)43(6,19-29(46)52)39(48-27)22(2)37-25(11-14-33(58)59)44(7,20-30(47)53)45(8,51-37)40-26(17-35(62)63)42(5,38(21)50-40)16-15-34(60)61/h18,23-26,40,51H,9-17,19-20H2,1-8H3,(H2,46,52)(H2,47,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/p-2/b27-18-,36-21+,37-22-/t23-,24-,25-,26+,40-,42-,43+,44+,45+/m1/s1

> <INCHI_KEY>
JJMDOVLPFPOLFZ-OMPOVKRGSA-L

> <FORMULA>
C45H60N6O12

> <MOLECULAR_WEIGHT>
877.006

> <EXACT_MASS>
876.428018556

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
123

> <JCHEM_AVERAGE_POLARIZABILITY>
91.0430094987807

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14,18-tetrakis(2-carboxyethyl)-19-(carboxymethyl)-3-[(C-hydroxycarbonimidoyl)methyl]-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-8-yl]ethanecarboximidate

> <JCHEM_LOGP>
0.6216745766908564

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.9338692807226185

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.534308604372422

> <JCHEM_PKA_STRONGEST_BASIC>
8.774948795580483

> <JCHEM_POLAR_SURFACE_AREA>
329.43

> <JCHEM_REFRACTIVITY>
272.2633000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14,18-tetrakis(2-carboxyethyl)-19-(carboxymethyl)-3-(C-hydroxycarbonimidoylmethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-8-yl]ethanecarboximidate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       9.781   1.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.459  -6.338   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.309  -0.475   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.889  -1.798   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.164  -2.488   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.657  -4.965   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.967  -7.005   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.109  -5.996   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.411  -1.050   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.188  -1.670   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.185  -8.476   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.305   0.486   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.466  -3.030   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.646  -8.532   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.783  -0.421   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.259  -0.637   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.489  -4.689   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.155   0.417   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.614  -3.343   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.486  -8.438   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.646   0.040   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.353  -5.084   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.867  -1.910   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.370  -0.365   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.906  -7.115   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.418  -3.582   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.314  -1.381   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.460   1.235   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -1.473  -4.621   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.847  -9.160   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       1.078   1.163   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.927  -3.086   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.924  -9.892   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      13.359   1.008   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      12.983  -4.314   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.946   1.064   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       5.229  -5.732   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       9.323  -1.344   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       2.404  -3.871   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       8.893  -3.798   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       4.834  -0.259   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      10.683  -2.065   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       0.923  -3.449   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       7.431  -6.899   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       7.697  -5.382   0.000  0.00  0.00           C+0
HETATM   46  N   UNK     0      -0.797  -6.004   0.000  0.00  0.00           N+0
HETATM   47  N   UNK     0      10.152  -8.342   0.000  0.00  0.00           N+0
HETATM   48  N   UNK     0       3.263  -2.594   0.000  0.00  0.00           N+0
HETATM   49  N   UNK     0       5.765   2.052   0.000  0.00  0.00           N+0
HETATM   50  N   UNK     0       8.216  -2.415   0.000  0.00  0.00           N+0
HETATM   51  N   UNK     0       6.336  -4.661   0.000  0.00  0.00           N+0
HETATM   52  O   UNK     0      -3.010  -4.515   0.000  0.00  0.00           O-1
HETATM   53  O   UNK     0       8.903 -10.699   0.000  0.00  0.00           O-1
HETATM   54  O   UNK     0       1.184   2.700   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       2.356   0.304   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0       4.110  -1.781   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0       4.206  -4.446   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0       3.742 -11.197   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0       1.385  -9.948   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      12.409   2.220   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      14.883   1.224   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      13.405  -2.834   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      14.054  -5.421   0.000  0.00  0.00           O+0
HETATM   64  H   UNK     0       2.626   1.863   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0       1.053  -0.381   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0       7.904  -0.229   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0       4.366  -7.090   0.000  0.00  0.00           H+0
HETATM   68  H   UNK     0       9.918  -5.039   0.000  0.00  0.00           H+0
HETATM   69  H   UNK     0       7.360  -3.651   0.000  0.00  0.00           H+0
CONECT    1   21                                                            
CONECT    2   22                                                            
CONECT    3   41                                                            
CONECT    4   41                                                            
CONECT    5   42                                                            
CONECT    6   43                                                            
CONECT    7   44                                                            
CONECT    8   45                                                            
CONECT    9   12   23                                                       
CONECT   10   13   24                                                       
CONECT   11   14   25                                                       
CONECT   12    9   31                                                       
CONECT   13   10   32                                                       
CONECT   14   11   33                                                       
CONECT   15   16   34                                                       
CONECT   16   15   42                                                       
CONECT   17   26   35                                                       
CONECT   18   27   28   64                                                  
CONECT   19   29   43                                                       
CONECT   20   30   44                                                       
CONECT   21    1   36   38                                                  
CONECT   22    2   37   39                                                  
CONECT   23    9   27   43   65                                             
CONECT   24   10   36   41   66                                             
CONECT   25   11   37   44   67                                             
CONECT   26   17   40   42   68                                             
CONECT   27   18   23   48                                                  
CONECT   28   18   41   49                                                  
CONECT   29   19   46   52                                                  
CONECT   30   20   47   53                                                  
CONECT   31   12   54   55                                                  
CONECT   32   13   56   57                                                  
CONECT   33   14   58   59                                                  
CONECT   34   15   60   61                                                  
CONECT   35   17   62   63                                                  
CONECT   36   21   24   49                                                  
CONECT   37   22   25   51                                                  
CONECT   38   21   42   50                                                  
CONECT   39   22   43   48                                                  
CONECT   40   26   45   50   69                                             
CONECT   41    3    4   24   28                                             
CONECT   42    5   16   26   38                                             
CONECT   43    6   19   23   39                                             
CONECT   44    7   20   25   45                                             
CONECT   45    8   40   44   51                                             
CONECT   46   29                                                            
CONECT   47   30                                                            
CONECT   48   27   39                                                       
CONECT   49   28   36                                                       
CONECT   50   38   40                                                       
CONECT   51   37   45                                                       
CONECT   52   29                                                            
CONECT   53   30                                                            
CONECT   54   31                                                            
CONECT   55   31                                                            
CONECT   56   32                                                            
CONECT   57   32                                                            
CONECT   58   33                                                            
CONECT   59   33                                                            
CONECT   60   34                                                            
CONECT   61   34                                                            
CONECT   62   35                                                            
CONECT   63   35                                                            
CONECT   64   18                                                            
CONECT   65   23                                                            
CONECT   66   24                                                            
CONECT   67   25                                                            
CONECT   68   26                                                            
CONECT   69   40                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  146    0
END

Synonyms

Value	Source
2-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-3-(Carboximidatomethyl)-4,9,14,18-tetrakis(2-carboxyethyl)-19-(carboxymethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1,.1,.1,]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-8-yl]ethanecarboximidic acid	Generator

Molecular Formula

C₄₅H₆₀N₆O₁₂

Average Mass

877.006

Monoisotopic Mass

876.428018556

IUPAC Name

2-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14,18-tetrakis(2-carboxyethyl)-19-(carboxymethyl)-3-[(C-hydroxycarbonimidoyl)methyl]-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-8-yl]ethanecarboximidate

Traditional Name

2-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14,18-tetrakis(2-carboxyethyl)-19-(carboxymethyl)-3-(C-hydroxycarbonimidoylmethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-8-yl]ethanecarboximidate

CAS Registry Number

Not Available

SMILES

[H]\C1=C2\N=C(\C(\C)=C3/N[C@@](C)([C@]4([H])N=C(\C(C)=C5\N=C1C(C)(C)[C@]5([H])CCC(O)=O)[C@](C)(CCC(O)=O)[C@@]4([H])CC(O)=O)[C@@](C)(CC([O-])=N)[C@]3([H])CCC(O)=O)[C@@](C)(CC([O-])=N)[C@]2([H])CCC(O)=O

InChI Identifier

InChI=1S/C45H62N6O12/c1-21-36-24(10-13-32(56)57)41(3,4)28(49-36)18-27-23(9-12-31(54)55)43(6,19-29(46)52)39(48-27)22(2)37-25(11-14-33(58)59)44(7,20-30(47)53)45(8,51-37)40-26(17-35(62)63)42(5,38(21)50-40)16-15-34(60)61/h18,23-26,40,51H,9-17,19-20H2,1-8H3,(H2,46,52)(H2,47,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,62,63)/p-2/b27-18-,36-21+,37-22-/t23-,24-,25-,26+,40-,42-,43+,44+,45+/m1/s1

InChI Key

JJMDOVLPFPOLFZ-OMPOVKRGSA-L

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	0.62	ChemAxon
pKa (Strongest Acidic)	3.53	ChemAxon
pKa (Strongest Basic)	8.77	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	329.43 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	272.26 m³·mol⁻¹	ChemAxon
Polarizability	91.04 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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	Proteobacteria	12	Human ; Human feces; Sheep ; Pig
Bacteria	Actinobacteria	5	Cattle ; Human

Exposure Sources

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for hydrogenobyrinate a,c-diamide (MMDBc0056031)

MOL for #<Metabolite:0x0000556b65c63218>

3D MOL for #<Metabolite:0x0000556b65c63218>

3D SDF for #<Metabolite:0x0000556b65c63218>

3D-SDF for #<Metabolite:0x0000556b65c63218>

PDB for #<Metabolite:0x0000556b65c63218>

3D PDB for #<Metabolite:0x0000556b65c63218>

SMILES for #<Metabolite:0x0000556b65c63218>

INCHI for #<Metabolite:0x0000556b65c63218>

Structure for #<Metabolite:0x0000556b65c63218>

3D Structure for #<Metabolite:0x0000556b65c63218>