NP-MRD: Showing NP-Card for Gomphrenin-I (NP0050748)

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Record Information

Version

2.0

Created at

2022-04-27 22:05:03 UTC

Updated at

2022-04-27 22:05:03 UTC

NP-MRD ID

NP0050748

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Gomphrenin-I

Description

Gomphrenin-I is found in Gomphrena globosa .

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282200052D          

 39 42  0  0  1  0            999 V2000
    4.0668    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -0.8853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -1.4984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1190   -2.2830    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6880   -2.4545    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -1.0568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0470   -2.0129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3020   -2.7976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5990   -1.3998    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6710   -2.8961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4161   -3.6807    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4780   -2.7246    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    0.8085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    2.2374    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0668    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812    1.1104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4957    0.6979    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4957   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102    1.1104    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2102    1.9354    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4957    2.3479    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7812    1.9354    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102    3.5854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9246    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9246    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 15 22  1  1  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
  9 25  1  6  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
  3 28  1  0  0  0  0
 29 28  1  6  0  0  0
 29 30  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 29 35  1  0  0  0  0
 34 36  1  1  0  0  0
 36 37  1  0  0  0  0
 33 38  1  1  0  0  0
 32 39  1  6  0  0  0
M  CHG  2  10   1  27  -1
M  END


  Mrv1652304282200052D          

 39 42  0  0  1  0            999 V2000
    4.0668    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -0.8853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -1.4984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1190   -2.2830    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6880   -2.4545    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -1.0568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0470   -2.0129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3020   -2.7976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5990   -1.3998    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6710   -2.8961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4161   -3.6807    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4780   -2.7246    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    0.8085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    2.2374    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0668    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812    1.1104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4957    0.6979    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4957   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102    1.1104    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2102    1.9354    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4957    2.3479    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7812    1.9354    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957    3.1729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2102    3.5854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9246    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9246    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 15 22  1  1  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
  9 25  1  6  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
  3 28  1  0  0  0  0
 29 28  1  6  0  0  0
 29 30  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 29 35  1  0  0  0  0
 34 36  1  1  0  0  0
 36 37  1  0  0  0  0
 33 38  1  1  0  0  0
 32 39  1  6  0  0  0
M  CHG  2  10   1  27  -1
M  END
> <DATABASE_ID>
NP0050748

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H]1O[C@@H](OC2=C(O)C=C3C[C@@H](C([O-])=O)\[N+](=C/C=C4\C[C@H](NC(=C4)C(O)=O)C(O)=O)C3=C2)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H26N2O13/c27-8-17-18(29)19(30)20(31)24(39-17)38-16-7-13-10(6-15(16)28)5-14(23(36)37)26(13)2-1-9-3-11(21(32)33)25-12(4-9)22(34)35/h1-3,6-7,12,14,17-20,24,27,29-31H,4-5,8H2,(H4,28,32,33,34,35,36,37)/t12-,14-,17-,18+,19-,20+,24+/m0/s1

> <INCHI_KEY>
YUDKHXMQDKVDGU-DRXTXWTKSA-N

> <FORMULA>
C24H26N2O13

> <MOLECULAR_WEIGHT>
550.473

> <EXACT_MASS>
550.143488905

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
52.429637381661315

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1E,2S)-1-{2-[(2S,4E)-2,6-dicarboxy-1,2,3,4-tetrahydropyridin-4-ylidene]ethylidene}-5-hydroxy-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1H-1lambda5-indol-1-ylium-2-carboxylate

> <ALOGPS_LOGP>
0.26

> <JCHEM_LOGP>
-5.378662464471747

> <ALOGPS_LOGS>
-3.10

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.129724520057778

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4551652263347763

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483953660473833

> <JCHEM_POLAR_SURFACE_AREA>
249.37999999999997

> <JCHEM_REFRACTIVITY>
149.70579999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.78e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1E,2S)-1-{2-[(2S,4E)-2,6-dicarboxy-2,3-dihydro-1H-pyridin-4-ylidene]ethylidene}-5-hydroxy-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1H-1lambda5-indol-1-ylium-2-carboxylate

> <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  O   UNK     0       7.591   4.383   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.126   4.089   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+1
HETATM   11  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.333  -1.652   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.698  -2.797   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.222  -4.262   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -1.284  -4.582   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -2.315  -3.437   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.839  -1.973   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -3.821  -3.757   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -4.297  -5.222   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -4.852  -2.613   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.253  -5.406   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       0.777  -6.871   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       2.759  -5.086   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -0.320   2.843   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -1.090   1.509   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -1.090   4.177   0.000  0.00  0.00           O-1
HETATM   28  O   UNK     0       7.591   1.303   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       8.925   2.073   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.259   1.303   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      10.259  -0.237   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      11.592   2.073   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      11.592   3.613   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      10.259   4.383   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       8.925   3.613   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      10.259   5.923   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      11.592   6.693   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      12.926   4.383   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      12.926   1.303   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   28                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    2                                                       
CONECT    8    6    9                                                       
CONECT    9    8   10   25                                                  
CONECT   10    9    5   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17   13                                                       
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   15   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25    9   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28    3   29                                                       
CONECT   29   28   30   35                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   39                                                  
CONECT   33   32   34   38                                                  
CONECT   34   33   35   36                                                  
CONECT   35   34   29                                                       
CONECT   36   34   37                                                       
CONECT   37   36                                                            
CONECT   38   33                                                            
CONECT   39   32                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₆N₂O₁₃

Average Mass

550.4730 Da

Monoisotopic Mass

550.14349 Da

IUPAC Name

(1E,2S)-1-{2-[(2S,4E)-2,6-dicarboxy-1,2,3,4-tetrahydropyridin-4-ylidene]ethylidene}-5-hydroxy-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1H-1lambda5-indol-1-ylium-2-carboxylate

Traditional Name

(1E,2S)-1-{2-[(2S,4E)-2,6-dicarboxy-2,3-dihydro-1H-pyridin-4-ylidene]ethylidene}-5-hydroxy-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1H-1lambda5-indol-1-ylium-2-carboxylate

CAS Registry Number

Not Available

SMILES

OC[C@@H]1O[C@@H](OC2=C(O)C=C3C[C@@H](C([O-])=O)\[N+](=C/C=C4\C[C@H](NC(=C4)C(O)=O)C(O)=O)C3=C2)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C24H26N2O13/c27-8-17-18(29)19(30)20(31)24(39-17)38-16-7-13-10(6-15(16)28)5-14(23(36)37)26(13)2-1-9-3-11(21(32)33)25-12(4-9)22(34)35/h1-3,6-7,12,14,17-20,24,27,29-31H,4-5,8H2,(H4,28,32,33,34,35,36,37)/t12-,14-,17-,18+,19-,20+,24+/m0/s1

InChI Key

YUDKHXMQDKVDGU-DRXTXWTKSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Gomphrena globosa	Plant	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	0.26	ALOGPS
logP	-5.4	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	1.46	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	249.38 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	149.71 m³·mol⁻¹	ChemAxon
Polarizability	52.43 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

Not Available

References

General References

Not Available

Showing NP-Card for Gomphrenin-I (NP0050748)

MOL for NP0050748 (Gomphrenin-I)

3D MOL for NP0050748 (Gomphrenin-I)

3D SDF for NP0050748 (Gomphrenin-I)

3D-SDF for NP0050748 (Gomphrenin-I)

PDB for NP0050748 (Gomphrenin-I)

3D PDB for NP0050748 (Gomphrenin-I)

SMILES for NP0050748 (Gomphrenin-I)

INCHI for NP0050748 (Gomphrenin-I)

Structure for NP0050748 (Gomphrenin-I)

3D Structure for NP0050748 (Gomphrenin-I)