MiMeDB: Showing metabocard for Sirolimus (MMDBc0047838)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:45:15 UTC

Update Date

2022-12-15 22:52:17 UTC

Metabolite ID

MMDBc0047838

Metabolite Identification

Common Name

Sirolimus

Description

Structure

MOL SDF PDB SMILES InChI

ChEBI
  Mrv0541 04191212152D          

 69 72  0  0  1  0            999 V2000
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M  END

ChEBI
  Mrv0541 04191212152D          

 69 72  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
MMDBc0047838

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(C[C@H](C)[C@]2([H])CC(=O)[C@H](C)\C=C(C)\[C@@H](O)[C@@H](OC)C(=O)[C@H](C)C[C@H](C)\C=C\C=C\C=C(C)\[C@H](C[C@]3([H])CC[C@@H](C)[C@@](O)(O3)C(=O)C(=O)N3CCCC[C@@]3([H])C(=O)O2)OC)CC[C@@H](O)[C@@H](C1)OC

> <INCHI_IDENTIFIER>
InChI=1S/C51H79NO13/c1-30-16-12-11-13-17-31(2)42(61-8)28-38-21-19-36(7)51(60,65-38)48(57)49(58)52-23-15-14-18-39(52)50(59)64-43(33(4)26-37-20-22-40(53)44(27-37)62-9)29-41(54)32(3)25-35(6)46(56)47(63-10)45(55)34(5)24-30/h11-13,16-17,25,30,32-34,36-40,42-44,46-47,53,56,60H,14-15,18-24,26-29H2,1-10H3/b13-11+,16-12+,31-17+,35-25+/t30-,32-,33+,34-,36-,37+,38+,39+,40-,42+,43+,44-,46-,47+,51-/m1/s1

> <INCHI_KEY>
QFJCIRLUMZQUOT-KLHQEZAJSA-N

> <FORMULA>
C51H79NO13

> <MOLECULAR_WEIGHT>
914.1719

> <EXACT_MASS>
913.555141619

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
100.46130388798993

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,9S,12S,15R,16E,18R,19R,21R,23S,24E,26E,28E,30S,32S,35R)-1,18-dihydroxy-12-[(2S)-1-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl]-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo[30.3.1.0⁴,⁹]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone

> <ALOGPS_LOGP>
4.85

> <JCHEM_LOGP>
7.450839822666669

> <ALOGPS_LOGS>
-5.72

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.368197872426823

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.963727691413887

> <JCHEM_PKA_STRONGEST_BASIC>
-3.040520864948703

> <JCHEM_POLAR_SURFACE_AREA>
195.42999999999998

> <JCHEM_REFRACTIVITY>
250.6632000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.73e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
sirolimus

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: ChEBI                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-12         0                                  
HETATM    1  C   UNK     0      14.446 -25.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.446 -27.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.112 -25.080   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      13.112 -28.160   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      11.778 -25.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.778 -27.390   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.780 -28.160   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      15.780 -29.700   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      14.446 -30.470   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      13.112 -29.700   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.779 -30.470   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.445 -29.700   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      18.447 -28.160   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      18.447 -29.700   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      17.113 -27.390   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      21.114 -28.160   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      21.114 -29.700   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      19.781 -27.390   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      19.781 -30.470   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      22.448 -25.850   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      22.448 -27.390   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      19.781 -25.850   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      25.116 -25.850   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      25.116 -27.390   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      23.782 -25.080   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      23.782 -28.160   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      13.112 -32.780   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      11.778 -32.010   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      13.112 -34.320   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      11.778 -35.089   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      10.445 -32.780   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.445 -34.319   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      14.446 -35.090   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      14.446 -36.630   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      13.112 -37.400   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      17.113 -36.630   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      15.779 -37.400   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      15.779 -38.939   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      13.112 -38.939   0.000  0.00  0.00           C+0
HETATM   40  H   UNK     0      19.624 -28.835   0.000  0.00  0.00           H+0
HETATM   41  C   UNK     0       9.111 -32.009   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      19.781 -32.010   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      18.447 -32.780   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      21.114 -32.780   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      21.114 -34.320   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      19.781 -35.090   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      22.448 -35.090   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      22.448 -36.630   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      21.114 -37.400   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      23.782 -34.320   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      23.782 -37.400   0.000  0.00  0.00           C+0
HETATM   52  H   UNK     0      13.112 -35.625   0.000  0.00  0.00           H+0
HETATM   53  C   UNK     0      17.101 -39.747   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      17.101 -41.536   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      23.782 -38.940   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      22.404 -39.680   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      21.114 -38.940   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      25.115 -36.630   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      18.333 -42.225   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      19.668 -41.301   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      21.179 -41.301   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      25.124 -39.659   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      22.469 -42.871   0.000  0.00  0.00           C+0
HETATM   64  H   UNK     0      22.469 -28.879   0.000  0.00  0.00           H+0
HETATM   65  O   UNK     0      26.449 -25.080   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      26.449 -28.160   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0      27.783 -27.390   0.000  0.00  0.00           C+0
HETATM   68  H   UNK     0      14.447 -28.967   0.000  0.00  0.00           H+0
HETATM   69  O   UNK     0      11.777 -33.601   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    7    4   68                                             
CONECT    3    1    5                                                       
CONECT    4    2    6   10                                                  
CONECT    5    3    6                                                       
CONECT    6    5    4                                                       
CONECT    7    2   15    8                                                  
CONECT    8    7                                                            
CONECT    9   10                                                            
CONECT   10    4    9   11                                                  
CONECT   11   12   10   28                                                  
CONECT   12   11                                                            
CONECT   13   15   18   14   40                                             
CONECT   14   13   19                                                       
CONECT   15   13    7                                                       
CONECT   16   21   18                                                       
CONECT   17   19                                                            
CONECT   18   13   16   22                                                  
CONECT   19   17   42   14                                                  
CONECT   20   25   21                                                       
CONECT   21   16   26   20   64                                             
CONECT   22   18                                                            
CONECT   23   24   25   65                                                  
CONECT   24   23   26   66                                                  
CONECT   25   23   20                                                       
CONECT   26   24   21                                                       
CONECT   27   29   28                                                       
CONECT   28   11   27   31   69                                             
CONECT   29   27   33   30   52                                             
CONECT   30   32   29                                                       
CONECT   31   28   32   41                                                  
CONECT   32   30   31                                                       
CONECT   33   29   34                                                       
CONECT   34   33   37   35                                                  
CONECT   35   34   39                                                       
CONECT   36   37                                                            
CONECT   37   36   38   34                                                  
CONECT   38   37   53                                                       
CONECT   39   35                                                            
CONECT   40   13                                                            
CONECT   41   31                                                            
CONECT   42   19   44   43                                                  
CONECT   43   42                                                            
CONECT   44   45   42                                                       
CONECT   45   44   47   46                                                  
CONECT   46   45                                                            
CONECT   47   48   45   50                                                  
CONECT   48   47   51   49                                                  
CONECT   49   48   57                                                       
CONECT   50   47                                                            
CONECT   51   48   55   58                                                  
CONECT   52   29                                                            
CONECT   53   38   54                                                       
CONECT   54   53   59                                                       
CONECT   55   51   56   62                                                  
CONECT   56   55   61                                                       
CONECT   57   49                                                            
CONECT   58   51                                                            
CONECT   59   54   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   56   63                                                  
CONECT   62   55                                                            
CONECT   63   61                                                            
CONECT   64   21                                                            
CONECT   65   23                                                            
CONECT   66   24   67                                                       
CONECT   67   66                                                            
CONECT   68    2                                                            
CONECT   69   28                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  144    0
END

Synonyms

Value	Source
(-)-Rapamycin	HMDB
Rapamycin	HMDB

Molecular Formula

C₅₁H₇₉NO₁₃

Average Mass

914.1719

Monoisotopic Mass

913.555141619

IUPAC Name

(1R,9S,12S,15R,16E,18R,19R,21R,23S,24E,26E,28E,30S,32S,35R)-1,18-dihydroxy-12-[(2S)-1-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]propan-2-yl]-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-11,36-dioxa-4-azatricyclo[30.3.1.0⁴,⁹]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone

Traditional Name

sirolimus

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C[C@H](C)[C@]2([H])CC(=O)[C@H](C)\C=C(C)\[C@@H](O)[C@@H](OC)C(=O)[C@H](C)C[C@H](C)\C=C\C=C\C=C(C)\[C@H](C[C@]3([H])CC[C@@H](C)[C@@](O)(O3)C(=O)C(=O)N3CCCC[C@@]3([H])C(=O)O2)OC)CC[C@@H](O)[C@@H](C1)OC

InChI Identifier

InChI=1S/C51H79NO13/c1-30-16-12-11-13-17-31(2)42(61-8)28-38-21-19-36(7)51(60,65-38)48(57)49(58)52-23-15-14-18-39(52)50(59)64-43(33(4)26-37-20-22-40(53)44(27-37)62-9)29-41(54)32(3)25-35(6)46(56)47(63-10)45(55)34(5)24-30/h11-13,16-17,25,30,32-34,36-40,42-44,46-47,53,56,60H,14-15,18-24,26-29H2,1-10H3/b13-11+,16-12+,31-17+,35-25+/t30-,32-,33+,34-,36-,37+,38+,39+,40-,42+,43+,44-,46-,47+,51-/m1/s1

InChI Key

QFJCIRLUMZQUOT-KLHQEZAJSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolide lactams. These are cyclic polyketides containing both a cyclic amide and a cyclic ester group.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolide lactams

Sub Class

Not Available

Direct Parent

Macrolide lactams

Alternative Parents

Substituents

Macrolide lactam
Alpha-amino acid ester
Macrolide
Alpha-amino acid or derivatives
Cyclohexanol
Oxane
Piperidine
Cyclic alcohol
Tertiary carboxylic acid amide
Cyclic ketone
Secondary alcohol
Carboxamide group
Carboxylic acid ester
Hemiacetal
Ketone
Lactam
Lactone
Organoheterocyclic compound
Azacycle
Carboxylic acid derivative
Oxacycle
Dialkyl ether
Ether
Monocarboxylic acid or derivatives
Organopnictogen compound
Alcohol
Organic oxygen compound
Carbonyl group
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Polyenes (LMPK06000003 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.0017 g/L	ALOGPS
logP	4.85	ALOGPS
logP	7.45	ChemAxon
logS	-5.7	ALOGPS
pKa (Strongest Acidic)	9.96	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	195.43 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	250.66 m³·mol⁻¹	ChemAxon
Polarizability	100.46 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03dj-0100000295-538de958471c20cea7a0	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001j-0632390280-a3032c3e232d4a2c7bdf	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01wr-0814113910-19c7692bfd13e245e54d	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0613322389-d91ce39dafa2a54bef2c	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-0202013090-dae32b81660bfccea140	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-000i-0925201100-d361305ce62d4f62a9ff	2016-09-14	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane

Biospecimen Locations

Kidney
Liver

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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

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
Human Kidney	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597

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

Sirolimus

METLIN ID

Not Available

PubChem Compound

46835353

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Ramirez-Gaona M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Feunang Y, Arndt D, Wishart DS: YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Res. 2017 Jan 4;45(D1):D440-D445. doi: 10.1093/nar/gkw1058. Epub 2016 Nov 28. [PubMed:27899612 ]

Showing metabocard for Sirolimus (MMDBc0047838)

MOL for #<Metabolite:0x00007fed14a99698>

3D MOL for #<Metabolite:0x00007fed14a99698>

3D SDF for #<Metabolite:0x00007fed14a99698>

3D-SDF for #<Metabolite:0x00007fed14a99698>

PDB for #<Metabolite:0x00007fed14a99698>

3D PDB for #<Metabolite:0x00007fed14a99698>

SMILES for #<Metabolite:0x00007fed14a99698>

INCHI for #<Metabolite:0x00007fed14a99698>

Structure for #<Metabolite:0x00007fed14a99698>

3D Structure for #<Metabolite:0x00007fed14a99698>