NP-MRD: Showing NP-Card for sirolimus (NP0215570)

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Record Information

Version

2.0

Created at

2022-09-05 15:13:59 UTC

Updated at

2022-09-05 15:13:59 UTC

NP-MRD ID

NP0215570

Secondary Accession Numbers

None

Natural Product Identification

Common Name

sirolimus

Description

Sirolimus, also known as rapamune or rapamycin, belongs to the class of organic compounds known as benzoic acids. These are organic Compounds containing a benzene ring which bears at least one carboxyl group. Sirolimus is a drug which is used for the prophylaxis of organ rejection in patients receiving renal transplants. sirolimus is found in Apis cerana, Streptomyces hygroscopicus and Streptomyces iranensis. sirolimus was first documented in 2004 (PMID: 15365568). Sirolimus is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 16103051) (PMID: 19387497).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652303062020292D          

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M  END

     RDKit          3D

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M  END


  Mrv1652303062020292D          

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M  END
> <DATABASE_ID>
NP0215570

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12CC[C@@H](C)[C@@](O)(O1)C(=O)C(=O)N1CCCC[C@@]1([H])C(=O)O[C@@]([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](C2)OC)[C@H](C)C[C@@H]1CC[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-HPLJOQBZSA-N

> <FORMULA>
C51H79NO13

> <MOLECULAR_WEIGHT>
914.187

> <EXACT_MASS>
913.555141608

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
144

> <JCHEM_AVERAGE_POLARIZABILITY>
101.03940623091498

> <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-[(2R)-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[30.3.1.0^{4,9}]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone

> <ALOGPS_LOGP>
4.85

> <JCHEM_LOGP>
7.45083982266667

> <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>
250.66320000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.73e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,9S,12S,15R,16E,18R,19R,21R,23S,24E,26E,28E,30S,32S,35R)-1,18-dihydroxy-12-[(2R)-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[30.3.1.0^{4,9}]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  O   UNK     0    8660.6448670.359   0.000  0.00  0.00           O+0
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HETATM    8  C   UNK     0    8669.9648671.144   0.000  0.00  0.00           C+0
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HETATM   29  C   UNK     0    8671.2868659.535   0.000  0.00  0.00           C+0
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HETATM   35  C   UNK     0    8664.6328660.301   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0    8664.6328661.849   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0    8663.3058662.623   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0    8663.3058664.171   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0    8660.6488668.818   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0    8659.3178669.583   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0    8660.6488665.730   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0    8657.9908667.262   0.000  0.00  0.00           C+0
HETATM   43  H   UNK     0    8661.9788663.408   0.000  0.00  0.00           H+0
HETATM   44  O   UNK     0    8661.9748661.856   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0    8660.3858662.771   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0    8665.9628662.615   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0    8670.8758656.611   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0    8673.9428659.535   0.000  0.00  0.00           C+0
HETATM   49  H   UNK     0    8668.6348670.375   0.000  0.00  0.00           H+0
HETATM   50  H   UNK     0    8663.3058670.379   0.000  0.00  0.00           H+0
HETATM   51  C   UNK     0    8661.9778674.227   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0    8660.6438673.457   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0    8660.6438671.917   0.000  0.00  0.00           C+0
HETATM   54  N   UNK     0    8661.9778671.147   0.000  0.00  0.00           N+0
HETATM   55  C   UNK     0    8663.3118671.917   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0    8663.3118673.457   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0    8660.6498667.258   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0    8659.3158666.488   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0    8659.3158664.948   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0    8660.6498664.178   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0    8661.9838664.948   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0    8661.9838666.488   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0    8672.6288674.218   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0    8671.2958673.448   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0    8671.2958671.908   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0    8672.6288671.138   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0    8673.9628671.908   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0    8673.9628673.448   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1   54   39                                                  
CONECT    3    4    5   55                                                  
CONECT    4    3                                                            
CONECT    5    6    3                                                       
CONECT    6    7   49   13    5                                             
CONECT    7    6    8   12                                                  
CONECT    8    7   65                                                       
CONECT    9   10   63                                                       
CONECT   10    9                                                            
CONECT   11   68                                                            
CONECT   12    7                                                            
CONECT   13   14    6                                                       
CONECT   14   15   16   13                                                  
CONECT   15   14                                                            
CONECT   16   17   18   14                                                  
CONECT   17   16                                                            
CONECT   18   19   16                                                       
CONECT   19   20   21   18                                                  
CONECT   20   19                                                            
CONECT   21   22   23   19                                                  
CONECT   22   21                                                            
CONECT   23   24   26   21                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   27   28   23                                                  
CONECT   27   26                                                            
CONECT   28   48   29   26                                                  
CONECT   29   30   28                                                       
CONECT   30   47   31   29                                                  
CONECT   31   32   30                                                       
CONECT   32   33   31                                                       
CONECT   33   34   32                                                       
CONECT   34   35   33                                                       
CONECT   35   36   34                                                       
CONECT   36   46   37   35                                                  
CONECT   37   44   38   36                                                  
CONECT   38   61   37                                                       
CONECT   39   40    2   57                                                  
CONECT   40   39                                                            
CONECT   41   57                                                            
CONECT   42   58                                                            
CONECT   43   61                                                            
CONECT   44   37   45                                                       
CONECT   45   44                                                            
CONECT   46   36                                                            
CONECT   47   30                                                            
CONECT   48   28                                                            
CONECT   49    6                                                            
CONECT   50   55                                                            
CONECT   51   52   56                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55    2                                                  
CONECT   55   56   54   50    3                                             
CONECT   56   51   55                                                       
CONECT   57   58   62   41   39                                             
CONECT   58   57   59   42                                                  
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62   43   38                                             
CONECT   62   57   61                                                       
CONECT   63   64   68    9                                                  
CONECT   64   63   65                                                       
CONECT   65   64   66    8                                                  
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   63   67   11                                                  
MASTER        0    0    0    0    0    0    0    0   68    0  142    0
END

View in JSmol

Synonyms

Value	Source
(-)-Rapamycin	ChEBI
(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[30.3.1.0(4,9)]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone	ChEBI
Antibiotic ay 22989	ChEBI
Rapamune	ChEBI
Rapamycin	ChEBI
Sirolimusum	ChEBI
Perceiva	HMDB
RAPA	HMDB
RPM	HMDB
Rapammune	HMDB
Rapamysin	HMDB
Sirolimus	MeSH

Chemical Formula

C₅₁H₇₉NO₁₃

Average Mass

914.1870 Da

Monoisotopic Mass

913.55514 Da

IUPAC Name

(1R,9S,12S,15R,16E,18R,19R,21R,23S,24E,26E,28E,30S,32S,35R)-1,18-dihydroxy-12-[(2R)-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[30.3.1.0^{4,9}]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC[C@@H](C)[C@@](O)(O1)C(=O)C(=O)N1CCCC[C@@]1([H])C(=O)O[C@@]([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](C2)OC)[C@H](C)C[C@@H]1CC[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-HPLJOQBZSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Apis cerana	LOTUS Database	35616633
Streptomyces hygroscopicus	LOTUS Database	35616633
Streptomyces iranensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzoic acids. These are organic Compounds containing a benzene ring which bears at least one carboxyl group.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Benzoic acids

Alternative Parents

Substituents

Benzoic acid
1,2,5-trisubstituted-imidazole
Benzoyl
Imidazolyl carboxylic acid derivative
Trisubstituted imidazole
Dicarboxylic acid or derivatives
N-substituted imidazole
Azole
Heteroaromatic compound
Imidazole
Thiophene
Carboxylic acid derivative
Carboxylic acid
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Organic oxide
Organic oxygen compound
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

imidazoles (CHEBI:4814 )
thiophenes (CHEBI:4814 )
dicarboxylic acid (CHEBI:4814 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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	101.04 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

External Links

HMDB ID

HMDB0015015

DrugBank ID

DB00877

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018055

Chemspider ID

10482078

KEGG Compound ID

C07909

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Rapamycin

METLIN ID

Not Available

PubChem Compound

5284616

PDB ID

Not Available

ChEBI ID

9168

Good Scents ID

Not Available

References

General References

Chan S: Targeting the mammalian target of rapamycin (mTOR): a new approach to treating cancer. Br J Cancer. 2004 Oct 18;91(8):1420-4. doi: 10.1038/sj.bjc.6602162. [PubMed:15365568 ]
Sun SY, Rosenberg LM, Wang X, Zhou Z, Yue P, Fu H, Khuri FR: Activation of Akt and eIF4E survival pathways by rapamycin-mediated mammalian target of rapamycin inhibition. Cancer Res. 2005 Aug 15;65(16):7052-8. doi: 10.1158/0008-5472.CAN-05-0917. [PubMed:16103051 ]
Graziani EI: Recent advances in the chemistry, biosynthesis and pharmacology of rapamycin analogs. Nat Prod Rep. 2009 May;26(5):602-9. doi: 10.1039/b804602f. Epub 2009 Mar 5. [PubMed:19387497 ]
LOTUS database [Link]

Showing NP-Card for sirolimus (NP0215570)

MOL for NP0215570 (sirolimus)

3D MOL for NP0215570 (sirolimus)

3D SDF for NP0215570 (sirolimus)

3D-SDF for NP0215570 (sirolimus)

PDB for NP0215570 (sirolimus)

3D PDB for NP0215570 (sirolimus)

SMILES for NP0215570 (sirolimus)

INCHI for NP0215570 (sirolimus)

Structure for NP0215570 (sirolimus)

3D Structure for NP0215570 (sirolimus)