NP-MRD: Showing NP-Card for Lyciumin B (NP0049193)

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Record Information

Version

2.0

Created at

2022-03-17 21:08:35 UTC

Updated at

2022-03-17 21:08:35 UTC

NP-MRD ID

NP0049193

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lyciumin B

Description

Lyciumin B is a weakly acidic compound (based on its pKa). Outside of the human body, lyciumin b has been detected, but not quantified in, a few different foods, such as coffee and coffee products, herbs and spices, and tea. Lyciumin B is found in Lycium chinense . This could make lyciumin b a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241210272D          

 65 71  0  0  0  0            999 V2000
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M  END


  Mrv0541 02241210272D          

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M  END
> <DATABASE_ID>
NP0049193

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C1NC(=O)C(NC(=O)C(CC2=CNC3=C2C=CC=C3)NC(=O)C2CCCN2C(=O)C2CCC(=O)N2)N2C=C(CC(NC(=O)C(CO)NC(=O)CNC1=O)C(O)=O)C1=C2C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C44H52N10O11/c1-22(2)36-41(61)46-19-35(57)48-31(21-55)39(59)50-30(44(64)65)17-24-20-54(32-11-6-4-9-26(24)32)37(42(62)51-36)52-38(58)29(16-23-18-45-27-10-5-3-8-25(23)27)49-40(60)33-12-7-15-53(33)43(63)28-13-14-34(56)47-28/h3-6,8-11,18,20,22,28-31,33,36-37,45,55H,7,12-17,19,21H2,1-2H3,(H,46,61)(H,47,56)(H,48,57)(H,49,60)(H,50,59)(H,51,62)(H,52,58)(H,64,65)

> <INCHI_KEY>
BWRVBFMWWHWLBW-UHFFFAOYSA-N

> <FORMULA>
C44H52N10O11

> <MOLECULAR_WEIGHT>
896.9441

> <EXACT_MASS>
896.381702556

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
89.78583153915443

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
11-(hydroxymethyl)-2-[3-(1H-indol-3-yl)-2-{[1-(5-oxopyrrolidine-2-carbonyl)pyrrolidin-2-yl]formamido}propanamido]-3,6,9,12-tetraoxo-5-(propan-2-yl)-1,4,7,10,13-pentaazatricyclo[14.6.1.0¹⁷,²²]tricosa-16(23),17(22),18,20-tetraene-14-carboxylic acid

> <ALOGPS_LOGP>
0.99

> <JCHEM_LOGP>
-1.7058901673333335

> <ALOGPS_LOGS>
-4.34

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.381917316151176

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.617383420486857

> <JCHEM_POLAR_SURFACE_AREA>
302.2599999999999

> <JCHEM_REFRACTIVITY>
227.655

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.10e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
11-(hydroxymethyl)-2-[3-(1H-indol-3-yl)-2-{[1-(5-oxopyrrolidine-2-carbonyl)pyrrolidin-2-yl]formamido}propanamido]-5-isopropyl-3,6,9,12-tetraoxo-1,4,7,10,13-pentaazatricyclo[14.6.1.0¹⁷,²²]tricosa-16(23),17(22),18,20-tetraene-14-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.756  -3.445   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.406  -4.255   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.945  -3.445   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.945  -1.958   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.406  -1.148   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.756  -1.958   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.188  -7.633   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.539  -6.823   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.891  -7.633   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       9.187  -4.796   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.836  -3.985   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       7.026  -5.336   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       5.539  -5.336   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.053  -5.336   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.243  -3.985   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.053  -2.770   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       3.243  -1.418   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       3.108   0.068   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       1.756   0.879   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       0.136   0.879   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.675  -0.472   0.000  0.00  0.00           O+0
HETATM   22  N   UNK     0       9.187  -1.688   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       7.836  -2.364   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.486  -1.688   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       5.134  -2.364   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      11.890  -1.688   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      10.539  -0.878   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.539   0.609   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       9.187   1.419   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       7.836   0.609   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       7.836  -0.878   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       6.486   1.419   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0       5.134   0.609   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0       3.783   1.419   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       3.783   3.040   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       7.836   3.715   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.486   3.040   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       5.134   3.715   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0      -2.161   2.229   0.000  0.00  0.00           N+0
HETATM   40  C   UNK     0      -0.675   2.229   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       0.812   2.905   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       1.082   4.662   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       0.001   5.202   0.000  0.00  0.00           C+0
HETATM   44  N   UNK     0       0.271   6.553   0.000  0.00  0.00           N+0
HETATM   45  O   UNK     0      -2.161   4.932   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      -2.972   3.580   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -4.593   3.580   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -5.404   2.229   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -6.890   2.634   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -7.026   4.120   0.000  0.00  0.00           C+0
HETATM   51  N   UNK     0      -5.674   4.797   0.000  0.00  0.00           N+0
HETATM   52  C   UNK     0      -6.485   6.147   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0      -5.674   7.498   0.000  0.00  0.00           O+0
HETATM   54  N   UNK     0      -9.052   7.363   0.000  0.00  0.00           N+0
HETATM   55  C   UNK     0      -7.972   6.147   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -8.782   4.797   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -10.404   5.067   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -10.539   6.688   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0     -11.890   7.498   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0       1.487   6.688   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       2.296   7.633   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       3.513   7.498   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       4.053   6.418   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0       3.243   5.337   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0       2.026   5.472   0.000  0.00  0.00           C+0
CONECT    1    2    6   15                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5   17                                                  
CONECT    7    8                                                            
CONECT    8    7    9   13                                                  
CONECT    9    8                                                            
CONECT   10   11                                                            
CONECT   11   10   12   23                                                  
CONECT   12   11   13                                                       
CONECT   13    8   12   14                                                  
CONECT   14   13   15                                                       
CONECT   15    1   14   16                                                  
CONECT   16   15   17                                                       
CONECT   17    6   16   18                                                  
CONECT   18   17   19   34                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   40                                                  
CONECT   21   20                                                            
CONECT   22   23   27                                                       
CONECT   23   11   22   24                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   27                                                            
CONECT   27   22   26   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   37                                                  
CONECT   33   32   34                                                       
CONECT   34   18   33   35                                                  
CONECT   35   34                                                            
CONECT   36   37                                                            
CONECT   37   32   36   38                                                  
CONECT   38   37                                                            
CONECT   39   40   46                                                       
CONECT   40   20   39   41                                                  
CONECT   41   40   42                                                       
CONECT   42   41   43   65                                                  
CONECT   43   42   44                                                       
CONECT   44   43   60                                                       
CONECT   45   46                                                            
CONECT   46   39   45   47                                                  
CONECT   47   46   48   51                                                  
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   47   50   52                                                  
CONECT   52   51   53   55                                                  
CONECT   53   52                                                            
CONECT   54   55   58                                                       
CONECT   55   52   54   56                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   54   57   59                                                  
CONECT   59   58                                                            
CONECT   60   44   61   65                                                  
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   42   60   64                                                  
MASTER        0    0    0    0    0    0    0    0   65    0  142    0
END

View in JSmol

Synonyms

Value	Source
3,6,9,12-Tetrahydroxy-2-{[1-hydroxy-2-({hydroxy[1-(5-hydroxy-3,4-dihydro-2H-pyrrole-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-(1H-indol-3-yl)propylidene]amino}-11-(hydroxymethyl)-5-(propan-2-yl)-1,4,7,10,13-pentaazatricyclo[14.6.1.0¹⁷,²²]tricosa-3,6,9,12,16(23),17,19,21-octaene-14-carboxylate	Generator

Chemical Formula

C₄₄H₅₂N₁₀O₁₁

Average Mass

896.9441 Da

Monoisotopic Mass

896.38170 Da

IUPAC Name

11-(hydroxymethyl)-2-[3-(1H-indol-3-yl)-2-{[1-(5-oxopyrrolidine-2-carbonyl)pyrrolidin-2-yl]formamido}propanamido]-3,6,9,12-tetraoxo-5-(propan-2-yl)-1,4,7,10,13-pentaazatricyclo[14.6.1.0¹⁷,²²]tricosa-16(23),17(22),18,20-tetraene-14-carboxylic acid

Traditional Name

11-(hydroxymethyl)-2-[3-(1H-indol-3-yl)-2-{[1-(5-oxopyrrolidine-2-carbonyl)pyrrolidin-2-yl]formamido}propanamido]-5-isopropyl-3,6,9,12-tetraoxo-1,4,7,10,13-pentaazatricyclo[14.6.1.0¹⁷,²²]tricosa-16(23),17(22),18,20-tetraene-14-carboxylic acid

CAS Registry Number

125756-66-3

SMILES

CC(C)C1NC(=O)C(NC(=O)C(CC2=CNC3=C2C=CC=C3)NC(=O)C2CCCN2C(=O)C2CCC(=O)N2)N2C=C(CC(NC(=O)C(CO)NC(=O)CNC1=O)C(O)=O)C1=C2C=CC=C1

InChI Identifier

InChI=1S/C44H52N10O11/c1-22(2)36-41(61)46-19-35(57)48-31(21-55)39(59)50-30(44(64)65)17-24-20-54(32-11-6-4-9-26(24)32)37(42(62)51-36)52-38(58)29(16-23-18-45-27-10-5-3-8-25(23)27)49-40(60)33-12-7-15-53(33)43(63)28-13-14-34(56)47-28/h3-6,8-11,18,20,22,28-31,33,36-37,45,55H,7,12-17,19,21H2,1-2H3,(H,46,61)(H,47,56)(H,48,57)(H,49,60)(H,50,59)(H,51,62)(H,52,58)(H,64,65)

InChI Key

BWRVBFMWWHWLBW-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Coffea arabica L.	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Coffea canephora	FooDB	Shmuel Yannai Dictionary of Food Compounds with CD-ROM: Additives, Flavors, and Ingredients. Chap...
Lycium chinense	Plant	KNApSAcK

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as cyclic peptides. These are compounds containing a cyclic moiety bearing a peptide backbone.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Cyclic peptides

Alternative Parents

Substituents

Cyclic alpha peptide
Alpha-amino acid or derivatives
3-alkylindole
Indole
Indole or derivatives
N-acylpyrrolidine
Pyrroline carboxylic acid or derivatives
Substituted pyrrole
Benzenoid
Pyrrole
Pyrrolidine
Heteroaromatic compound
Pyrroline
Tertiary carboxylic acid amide
Cyclic carboximidic acid
Lactim
Carboxamide group
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidic acid derivative
Organoheterocyclic compound
Azacycle
Carboximidic acid
Carboxylic acid
Monocarboxylic acid or derivatives
Polyol
Organic oxide
Organopnictogen compound
Carbonyl group
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Primary alcohol
Alcohol
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	0.99	ALOGPS
logP	-1.7	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	3.62	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	302.26 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	227.66 m³·mol⁻¹	ChemAxon
Polarizability	89.79 Å³	ChemAxon
Number of Rings	7	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

HMDB0038673

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB018073

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

14430292

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Lyciumin B (NP0049193)

MOL for NP0049193 (Lyciumin B)

3D MOL for NP0049193 (Lyciumin B)

3D SDF for NP0049193 (Lyciumin B)

3D-SDF for NP0049193 (Lyciumin B)

PDB for NP0049193 (Lyciumin B)

3D PDB for NP0049193 (Lyciumin B)

SMILES for NP0049193 (Lyciumin B)

INCHI for NP0049193 (Lyciumin B)

Structure for NP0049193 (Lyciumin B)

3D Structure for NP0049193 (Lyciumin B)