NP-MRD: Showing NP-Card for Odulin (NP0070253)

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Record Information

Version

2.0

Created at

2022-04-28 15:32:48 UTC

Updated at

2022-04-28 15:32:48 UTC

NP-MRD ID

NP0070253

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Odulin

Description

(2R,3R,10S,12R)-4-methyl-11,16,18-trioxa-4-azapentacyclo[11.7.0.0²,¹⁰.0³,⁷.0¹⁵,¹⁹]Icosa-1(20),7,13,15(19)-tetraen-12-ol belongs to the class of organic compounds known as homolycorine-type amaryllidaceae alkaloids. These are amaryllidaceae alkaloids compounds containing the homolycorine skeleton, made up of a [3,4-g]benzopyranone ring due to the oxidation of the hydroxyl group at the C6. They are biogenetically formed through a restructuring of lycorine-type alkaloids. Odulin is found in Narcissus pseudonarcissus subsp.pseudonarcissus. Based on a literature review very few articles have been published on (2R,3R,10S,12R)-4-methyl-11,16,18-trioxa-4-azapentacyclo[11.7.0.0²,¹⁰.0³,⁷.0¹⁵,¹⁹]Icosa-1(20),7,13,15(19)-tetraen-12-ol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 41 45  0  0  0  0  0  0  0  0999 V2000
    2.0226    2.1200    1.3826 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5366    1.0201    0.6353 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6043    1.3490   -0.2475 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7394    0.1926   -1.1772 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4554   -0.5777   -0.9389 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0532   -1.7796   -1.2927 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7039   -2.2145   -0.8717 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6896   -1.8769    0.6324 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2628   -2.5534    1.3322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5349   -2.4371    0.8600 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4191   -2.8382    1.8674 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8114   -1.0359    0.4709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1480   -0.7482    0.1808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5279    0.5103   -0.1924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5637    1.4934   -0.2774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2355    1.1970    0.0135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8530   -0.0612    0.3872 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5517   -0.3795    0.6973 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5443    0.3041   -0.1510 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1837    2.6504   -0.6650 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5686    2.4824   -0.5441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7448    1.0932   -0.5358 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3645    1.7796    2.1915 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5705    2.9154    0.7551 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9024    2.6056    1.8772 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5383    1.4804    0.3627 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4660    2.3134   -0.7806 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6191   -0.4367   -0.8963 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8113    0.4836   -2.2396 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6755   -2.4205   -1.8631 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5210   -3.2853   -1.0314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0293   -1.5669   -1.3995 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6818   -2.1705    1.0430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7528   -3.1118   -0.0086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8778   -3.6814    1.6677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9017   -1.5199    0.2480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4747    1.9561   -0.0501 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7678   -0.1246    1.7858 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0904    0.9878   -0.9183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9539    2.9751    0.3831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0658    2.9101   -1.4381 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 17  2  0
 17 16  1  0
 16 15  2  0
 15 20  1  0
 20 21  1  0
 21 22  1  0
 22 14  1  0
 14 13  2  0
 17 18  1  0
 18 19  1  0
 19  2  1  0
 19  5  1  0
 18  8  1  0
 13 12  1  0
 14 15  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  3 26  1  0
  3 27  1  0
  4 28  1  0
  4 29  1  0
  6 30  1  0
  7 31  1  0
  7 32  1  0
  8 33  1  1
 10 34  1  6
 11 35  1  0
 16 37  1  0
 21 40  1  0
 21 41  1  0
 13 36  1  0
 18 38  1  1
 19 39  1  6
M  END


  Mrv1652304282217332D          

 22 26  0  0  1  0            999 V2000
   -0.6931   -1.1154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9734   -1.8914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4416   -2.5221    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3705   -2.3768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6508   -1.6009    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1190   -0.9702    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3993   -0.1943    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2114   -0.0491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7433   -0.6798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4630   -1.4557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3243    0.7682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5819    1.1280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0103    0.5332    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8070    0.6461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7219   -3.2980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7855   -2.0366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3173   -1.4059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0370   -0.6299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2249   -0.4847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6884   -0.1236    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3712   -0.5866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1419   -1.3791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  6  0  0  0
  5  6  1  0  0  0  0
  6  1  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  5 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  7 13  1  1  0  0  0
 13 14  1  0  0  0  0
  3 15  1  1  0  0  0
  2 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
  1 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 17 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0070253

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CCC2=CC[C@@H]3O[C@@H](O)C4=C(C=C5OCOC5=C4)[C@@H]3[C@@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C17H19NO4/c1-18-5-4-9-2-3-12-15(16(9)18)10-6-13-14(21-8-20-13)7-11(10)17(19)22-12/h2,6-7,12,15-17,19H,3-5,8H2,1H3/t12-,15-,16-,17+/m0/s1

> <INCHI_KEY>
FUVJDWFLSZRIQX-OSMBCOQSSA-N

> <FORMULA>
C17H19NO4

> <MOLECULAR_WEIGHT>
301.342

> <EXACT_MASS>
301.131408096

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
31.842840066874476

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R,3R,10S,12R)-4-methyl-11,16,18-trioxa-4-azapentacyclo[11.7.0.0^{2,10}.0^{3,7}.0^{15,19}]icosa-1(13),7,14,19-tetraen-12-ol

> <ALOGPS_LOGP>
1.25

> <JCHEM_LOGP>
1.3602325193333336

> <ALOGPS_LOGS>
-2.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.567091924106853

> <JCHEM_PKA_STRONGEST_BASIC>
8.224475354322974

> <JCHEM_POLAR_SURFACE_AREA>
51.16000000000001

> <JCHEM_REFRACTIVITY>
80.75520000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.94e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,10S,12R)-4-methyl-11,16,18-trioxa-4-azapentacyclo[11.7.0.0^{2,10}.0^{3,7}.0^{15,19}]icosa-1(13),7,14,19-tetraen-12-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -1.294  -2.082   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.817  -3.531   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.824  -4.708   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.692  -4.437   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.215  -2.988   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.222  -1.811   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.745  -0.363   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.261  -0.092   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.254  -1.269   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.731  -2.717   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.472   1.434   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.086   2.106   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       0.019   0.995   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -1.506   1.206   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.348  -6.156   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -3.333  -3.802   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.326  -2.624   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.802  -1.176   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.287  -0.905   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -5.018  -0.231   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -6.293  -1.095   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -5.865  -2.574   0.000  0.00  0.00           O+0
CONECT    1    2    6   19                                                  
CONECT    2    1    3   16                                                  
CONECT    3    2    4   15                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    8   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    7   14                                                  
CONECT   14   13                                                            
CONECT   15    3                                                            
CONECT   16    2   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18    1                                                       
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   17                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₁₉NO₄

Average Mass

301.3420 Da

Monoisotopic Mass

301.13141 Da

IUPAC Name

(2R,3R,10S,12R)-4-methyl-11,16,18-trioxa-4-azapentacyclo[11.7.0.0^{2,10}.0^{3,7}.0^{15,19}]icosa-1(13),7,14,19-tetraen-12-ol

Traditional Name

(2R,3R,10S,12R)-4-methyl-11,16,18-trioxa-4-azapentacyclo[11.7.0.0^{2,10}.0^{3,7}.0^{15,19}]icosa-1(13),7,14,19-tetraen-12-ol

CAS Registry Number

Not Available

SMILES

CN1CCC2=CC[C@@H]3O[C@@H](O)C4=C(C=C5OCOC5=C4)[C@@H]3[C@@H]12

InChI Identifier

InChI=1S/C17H19NO4/c1-18-5-4-9-2-3-12-15(16(9)18)10-6-13-14(21-8-20-13)7-11(10)17(19)22-12/h2,6-7,12,15-17,19H,3-5,8H2,1H3/t12-,15-,16-,17+/m0/s1

InChI Key

FUVJDWFLSZRIQX-OSMBCOQSSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Narcissus pseudonarcissus subsp.pseudonarcissus	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as homolycorine-type amaryllidaceae alkaloids. These are amaryllidaceae alkaloids compounds containing the homolycorine skeleton, made up of a [3,4-g]benzopyranone ring due to the oxidation of the hydroxyl group at the C6. They are biogenetically formed through a restructuring of lycorine-type alkaloids.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Amaryllidaceae alkaloids

Sub Class

Homolycorine-type amaryllidaceae alkaloids

Direct Parent

Homolycorine-type amaryllidaceae alkaloids

Alternative Parents

Substituents

Homolycorine skeleton
2-benzopyran
Isochromane
Benzopyran
Indole or derivatives
Benzodioxole
Aralkylamine
Benzenoid
N-alkylpyrrolidine
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Hemiacetal
Oxacycle
Azacycle
Organoheterocyclic compound
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Amine
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	1.25	ALOGPS
logP	1.36	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	11.57	ChemAxon
pKa (Strongest Basic)	8.22	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	51.16 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	80.76 m³·mol⁻¹	ChemAxon
Polarizability	31.84 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

162876475

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Odulin (NP0070253)

MOL for NP0070253 (Odulin)

3D MOL for NP0070253 (Odulin)

3D SDF for NP0070253 (Odulin)

3D-SDF for NP0070253 (Odulin)

PDB for NP0070253 (Odulin)

3D PDB for NP0070253 (Odulin)

SMILES for NP0070253 (Odulin)

INCHI for NP0070253 (Odulin)

Structure for NP0070253 (Odulin)

3D Structure for NP0070253 (Odulin)