NP-MRD: Showing NP-Card for Lyciumin C (NP0049702)

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Record Information

Version

2.0

Created at

2022-03-17 21:16:43 UTC

Updated at

2022-03-17 21:16:43 UTC

NP-MRD ID

NP0049702

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lyciumin C

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305221920442D          

 78 84  0  0  1  0            999 V2000
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M  END


  Mrv1652305221920442D          

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 30 17  1  0  0  0  0
 31 11  2  0  0  0  0
 31 29  1  0  0  0  0
 32 18  1  0  0  0  0
 33 21  1  6  0  0  0
 34 22  1  0  0  0  0
 35 23  1  0  0  0  0
 36 25  1  6  0  0  0
 37 12  2  0  0  0  0
 37 31  1  0  0  0  0
 38 13  1  0  0  0  0
 39 19  1  0  0  0  0
 40 26  1  6  0  0  0
 42 33  1  0  0  0  0
 43 34  1  0  0  0  0
 44 36  1  0  0  0  0
 38 45  1  6  0  0  0
 46 40  1  0  0  0  0
 47 41  1  0  0  0  0
 32 48  1  6  0  0  0
 35 49  1  1  0  0  0
 50 32  1  0  0  0  0
 50 39  2  0  0  0  0
 34 51  1  1  0  0  0
 51 45  2  0  0  0  0
 52 33  1  0  0  0  0
 52 46  2  0  0  0  0
 53 35  1  0  0  0  0
 53 44  2  0  0  0  0
 54 36  1  0  0  0  0
 54 42  2  0  0  0  0
 55 40  1  0  0  0  0
 55 47  2  0  0  0  0
 56 41  1  4  0  0  0
 56 43  2  0  0  0  0
 57 20  1  0  0  0  0
 57 38  1  0  0  0  0
 57 48  1  0  0  0  0
 58 24  1  0  0  0  0
 58 37  1  0  0  0  0
 58 41  1  0  0  0  0
 59 25  1  0  0  0  0
 60 30  1  0  0  0  0
 61 39  1  0  0  0  0
 42 62  1  4  0  0  0
 63 43  1  0  0  0  0
 44 64  1  4  0  0  0
 45 65  1  4  0  0  0
 46 66  1  4  0  0  0
 47 67  1  4  0  0  0
 68 48  2  0  0  0  0
 69 49  2  0  0  0  0
 70 49  1  0  0  0  0
 32 71  1  1  0  0  0
 33 72  1  1  0  0  0
 34 73  1  6  0  0  0
 35 74  1  1  0  0  0
 36 75  1  6  0  0  0
 38 76  1  1  0  0  0
 40 77  1  1  0  0  0
 78 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0049702

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@](CC1=CC=C(O)C=C1)(N=C(O)[C@]1([H])CCCN1C(=O)[C@]1([H])CCC(O)=N1)C(O)=NC1([H])N2C=C(C[C@@]([H])(N=C(O)[C@@]([H])(CO)N=C(O)[C@]([H])(CC3=CC=CC=C3)N=C(O)[C@@]([H])(N=C1O)C(C)C)C(O)=O)C1=CC=CC=C21

> <INCHI_IDENTIFIER>
InChI=1S/C49H57N9O12/c1-26(2)40-46(66)52-33(21-27-9-4-3-5-10-27)42(62)54-36(25-59)44(64)53-35(49(69)70)23-29-24-58(37-12-7-6-11-31(29)37)41(47(67)55-40)56-43(63)34(22-28-14-16-30(60)17-15-28)51-45(65)38-13-8-20-57(38)48(68)32-18-19-39(61)50-32/h3-7,9-12,14-17,24,26,32-36,38,40-41,59-60H,8,13,18-23,25H2,1-2H3,(H,50,61)(H,51,65)(H,52,66)(H,53,64)(H,54,62)(H,55,67)(H,56,63)(H,69,70)/t32-,33-,34-,35+,36+,38-,40-,41?/m0/s1

> <INCHI_KEY>
JJVYOOBAXDVVNT-PVSXJMBXSA-N

> <FORMULA>
C49H57N9O12

> <MOLECULAR_WEIGHT>
964.03

> <EXACT_MASS>
963.412668333

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
127

> <JCHEM_AVERAGE_POLARIZABILITY>
99.2410771246135

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5S,8S,11R,14R)-8-benzyl-3,6,9,12-tetrahydroxy-2-{[(2S)-1-hydroxy-2-({hydroxy[(2S)-1-[(2S)-5-hydroxy-3,4-dihydro-2H-pyrrole-2-carbonyl]pyrrolidin-2-yl]methylidene}amino)-3-(4-hydroxyphenyl)propylidene]amino}-11-(hydroxymethyl)-5-(propan-2-yl)-1,4,7,10,13-pentaazatricyclo[14.6.1.0^{17,22}]tricosa-3,6,9,12,16(23),17,19,21-octaene-14-carboxylic acid

> <ALOGPS_LOGP>
2.04

> <JCHEM_LOGP>
5.854102017

> <ALOGPS_LOGS>
-3.86

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.9968229096803602

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.327141759019749

> <JCHEM_POLAR_SURFACE_AREA>
331.13

> <JCHEM_REFRACTIVITY>
251.31420000000017

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.33e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5S,8S,11R,14R)-8-benzyl-3,6,9,12-tetrahydroxy-2-{[(2S)-1-hydroxy-2-({hydroxy[(2S)-1-[(2S)-5-hydroxy-3,4-dihydro-2H-pyrrole-2-carbonyl]pyrrolidin-2-yl]methylidene}amino)-3-(4-hydroxyphenyl)propylidene]amino}-11-(hydroxymethyl)-5-isopropyl-1,4,7,10,13-pentaazatricyclo[14.6.1.0^{17,22}]tricosa-3,6,9,12,16(23),17,19,21-octaene-14-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       4.858   7.014   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.758   5.369   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.816   4.720   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.391   3.292   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.291   4.937   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.455  -0.680   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.239   0.844   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.504   8.791   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.442   2.079   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.658   3.724   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.243  -1.630   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.810   1.420   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.928   7.363   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      15.115   1.399   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.943   3.795   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      16.498   2.076   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      15.326   4.472   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.000   9.105   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      15.446   9.634   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.040   8.686   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.033   1.083   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      12.454   1.582   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.880  -3.334   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.506  -0.693   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.431  -3.132   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.283   5.585   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.083   2.296   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      13.837   2.259   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.456  -1.905   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      16.604   3.613   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.814  -1.055   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      14.055   7.566   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.557   1.299   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      11.176   2.442   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.224  -3.643   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       3.912  -2.712   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       9.739   0.882   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      10.109   6.374   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      16.396   8.421   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       5.232   4.373   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       7.132   1.948   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       3.507   0.087   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       9.793   1.765   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       3.807  -4.248   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      10.004   4.838   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       4.657   2.944   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       7.707   3.376   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      12.843   6.617   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       7.001  -4.972   0.000  0.00  0.00           C+0
HETATM   50  N   UNK     0      15.536   7.144   0.000  0.00  0.00           N+0
HETATM   51  N   UNK     0      11.282   3.978   0.000  0.00  0.00           N+0
HETATM   52  N   UNK     0       3.132   2.728   0.000  0.00  0.00           N+0
HETATM   53  N   UNK     0       5.235  -4.824   0.000  0.00  0.00           N+0
HETATM   54  N   UNK     0       2.932  -1.342   0.000  0.00  0.00           N+0
HETATM   55  N   UNK     0       6.757   4.589   0.000  0.00  0.00           N+0
HETATM   56  N   UNK     0       8.515   2.625   0.000  0.00  0.00           N+0
HETATM   57  N   UNK     0      11.414   7.192   0.000  0.00  0.00           N+0
HETATM   58  N   UNK     0       8.081   0.736   0.000  0.00  0.00           N+0
HETATM   59  O   UNK     0       1.326  -2.059   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      17.987   4.289   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      17.935   8.477   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0       5.032   0.303   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0       9.687   0.229   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       2.502  -5.066   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       8.620   4.161   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       5.607   1.732   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0       9.231   3.593   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      13.059   5.092   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0       6.238  -6.310   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0       8.541  -4.964   0.000  0.00  0.00           O+0
HETATM   71  H   UNK     0      14.351   6.055   0.000  0.00  0.00           H+0
HETATM   72  H   UNK     0       1.608   2.512   0.000  0.00  0.00           H+0
HETATM   73  H   UNK     0       9.898   3.301   0.000  0.00  0.00           H+0
HETATM   74  H   UNK     0       5.446  -2.313   0.000  0.00  0.00           H+0
HETATM   75  H   UNK     0       4.437  -1.264   0.000  0.00  0.00           H+0
HETATM   76  H   UNK     0       8.692   5.771   0.000  0.00  0.00           H+0
HETATM   77  H   UNK     0       5.808   5.801   0.000  0.00  0.00           H+0
HETATM   78  H   UNK     0       6.556   0.519   0.000  0.00  0.00           H+0
CONECT    1   26                                                            
CONECT    2   26                                                            
CONECT    3    4    5                                                       
CONECT    4    3    9                                                       
CONECT    5    3   10                                                       
CONECT    6    7   11                                                       
CONECT    7    6   12                                                       
CONECT    8   13   20                                                       
CONECT    9    4   27                                                       
CONECT   10    5   27                                                       
CONECT   11    6   31                                                       
CONECT   12    7   37                                                       
CONECT   13    8   38                                                       
CONECT   14   16   28                                                       
CONECT   15   17   28                                                       
CONECT   16   14   30                                                       
CONECT   17   15   30                                                       
CONECT   18   19   32                                                       
CONECT   19   18   39                                                       
CONECT   20    8   57                                                       
CONECT   21   27   33                                                       
CONECT   22   28   34                                                       
CONECT   23   29   35                                                       
CONECT   24   29   58                                                       
CONECT   25   36   59                                                       
CONECT   26    1    2   40                                                  
CONECT   27    9   10   21                                                  
CONECT   28   14   15   22                                                  
CONECT   29   23   24   31                                                  
CONECT   30   16   17   60                                                  
CONECT   31   11   29   37                                                  
CONECT   32   18   48   50   71                                             
CONECT   33   21   42   52   72                                             
CONECT   34   22   43   51   73                                             
CONECT   35   23   49   53   74                                             
CONECT   36   25   44   54   75                                             
CONECT   37   12   31   58                                                  
CONECT   38   13   45   57   76                                             
CONECT   39   19   50   61                                                  
CONECT   40   26   46   55   77                                             
CONECT   41   47   56   58   78                                             
CONECT   42   33   54   62                                                  
CONECT   43   34   56   63                                                  
CONECT   44   36   53   64                                                  
CONECT   45   38   51   65                                                  
CONECT   46   40   52   66                                                  
CONECT   47   41   55   67                                                  
CONECT   48   32   57   68                                                  
CONECT   49   35   69   70                                                  
CONECT   50   32   39                                                       
CONECT   51   34   45                                                       
CONECT   52   33   46                                                       
CONECT   53   35   44                                                       
CONECT   54   36   42                                                       
CONECT   55   40   47                                                       
CONECT   56   41   43                                                       
CONECT   57   20   38   48                                                  
CONECT   58   24   37   41                                                  
CONECT   59   25                                                            
CONECT   60   30                                                            
CONECT   61   39                                                            
CONECT   62   42                                                            
CONECT   63   43                                                            
CONECT   64   44                                                            
CONECT   65   45                                                            
CONECT   66   46                                                            
CONECT   67   47                                                            
CONECT   68   48                                                            
CONECT   69   49                                                            
CONECT   70   49                                                            
CONECT   71   32                                                            
CONECT   72   33                                                            
CONECT   73   34                                                            
CONECT   74   35                                                            
CONECT   75   36                                                            
CONECT   76   38                                                            
CONECT   77   40                                                            
CONECT   78   41                                                            
MASTER        0    0    0    0    0    0    0    0   78    0  168    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₉H₅₇N₉O₁₂

Average Mass

964.0300 Da

Monoisotopic Mass

963.41267 Da

IUPAC Name

(5S,8S,11R,14R)-8-benzyl-3,6,9,12-tetrahydroxy-2-{[(2S)-1-hydroxy-2-({hydroxy[(2S)-1-[(2S)-5-hydroxy-3,4-dihydro-2H-pyrrole-2-carbonyl]pyrrolidin-2-yl]methylidene}amino)-3-(4-hydroxyphenyl)propylidene]amino}-11-(hydroxymethyl)-5-(propan-2-yl)-1,4,7,10,13-pentaazatricyclo[14.6.1.0^{17,22}]tricosa-3,6,9,12,16(23),17,19,21-octaene-14-carboxylic acid

Traditional Name

(5S,8S,11R,14R)-8-benzyl-3,6,9,12-tetrahydroxy-2-{[(2S)-1-hydroxy-2-({hydroxy[(2S)-1-[(2S)-5-hydroxy-3,4-dihydro-2H-pyrrole-2-carbonyl]pyrrolidin-2-yl]methylidene}amino)-3-(4-hydroxyphenyl)propylidene]amino}-11-(hydroxymethyl)-5-isopropyl-1,4,7,10,13-pentaazatricyclo[14.6.1.0^{17,22}]tricosa-3,6,9,12,16(23),17,19,21-octaene-14-carboxylic acid

CAS Registry Number

150394-23-3

SMILES

[H][C@@](CC1=CC=C(O)C=C1)(N=C(O)[C@]1([H])CCCN1C(=O)[C@]1([H])CCC(O)=N1)C(O)=NC1([H])N2C=C(C[C@@]([H])(N=C(O)[C@@]([H])(CO)N=C(O)[C@]([H])(CC3=CC=CC=C3)N=C(O)[C@@]([H])(N=C1O)C(C)C)C(O)=O)C1=CC=CC=C21

InChI Identifier

InChI=1S/C49H57N9O12/c1-26(2)40-46(66)52-33(21-27-9-4-3-5-10-27)42(62)54-36(25-59)44(64)53-35(49(69)70)23-29-24-58(37-12-7-6-11-31(29)37)41(47(67)55-40)56-43(63)34(22-28-14-16-30(60)17-15-28)51-45(65)38-13-8-20-57(38)48(68)32-18-19-39(61)50-32/h3-7,9-12,14-17,24,26,32-36,38,40-41,59-60H,8,13,18-23,25H2,1-2H3,(H,50,61)(H,51,65)(H,52,66)(H,53,64)(H,54,62)(H,55,67)(H,56,63)(H,69,70)/t32-,33-,34-,35+,36+,38-,40-,41?/m0/s1

InChI Key

JJVYOOBAXDVVNT-PVSXJMBXSA-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...

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
Cyclic alpha peptide
Tyrosine or derivatives
Phenylalanine or derivatives
Proline or derivatives
N-acyl-alpha amino acid or derivatives
Macrolactam
Alpha-amino acid amide
3-alkylindole
Amphetamine or derivatives
Alpha-amino acid or derivatives
N-substituted-alpha-amino acid
Indole or derivatives
Indole
Pyrrolidine-2-carboxamide
Pyrrolidine carboxylic acid or derivatives
N-acylpyrrolidine
1-hydroxy-2-unsubstituted benzenoid
Phenol
Fatty acyl
Benzenoid
2-pyrrolidone
Pyrrolidone
Fatty amide
Monocyclic benzene moiety
Heteroaromatic compound
Tertiary carboxylic acid amide
Pyrrolidine
Pyrrole
Secondary carboxylic acid amide
Lactam
Carboxamide group
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
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	2.04	ALOGPS
logP	5.85	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	2.33	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	331.13 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	251.31 m³·mol⁻¹	ChemAxon
Polarizability	99.24 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB020498

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

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Lyciumin C (NP0049702)

MOL for NP0049702 (Lyciumin C)

3D MOL for NP0049702 (Lyciumin C)

3D SDF for NP0049702 (Lyciumin C)

3D-SDF for NP0049702 (Lyciumin C)

PDB for NP0049702 (Lyciumin C)

3D PDB for NP0049702 (Lyciumin C)

SMILES for NP0049702 (Lyciumin C)

INCHI for NP0049702 (Lyciumin C)

Structure for NP0049702 (Lyciumin C)

3D Structure for NP0049702 (Lyciumin C)