NP-MRD: Showing NP-Card for Glycodesoxycholic acid (NP0002830)

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Record Information

Version

2.0

Created at

2020-11-23 19:41:30 UTC

Updated at

2021-08-12 19:52:16 UTC

NP-MRD ID

NP0002830

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Glycodesoxycholic acid

Provided By

BMRB

Description

Glycodeoxycholic acid is also known as deoxycholylglycine or GDCA. Glycodesoxycholic acid is found in Streptomyces nigra and Trypanosoma brucei. Glycodesoxycholic acid was first documented in 2012 (PMID: 22359652). Based on a literature review a small amount of articles have been published on glycodeoxycholic acid (PMID: 23892997).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


     RDKit          2D

 75 78  0  0  0  0  0  0  0  0999 V2000
    3.7030    1.6549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9478   -4.2896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1881   -2.9741    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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 29 71  1  6
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 32 75  1  0
M  END

NP0002830
     RDKit          3D

 75 78  0  0  0  0  0  0  0  0999 V2000
    3.1252   -2.9178    0.3199 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7721   -1.7217   -0.4776 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3521   -0.4197    0.0076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8450   -0.3757    0.0349 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2633    0.9542    0.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4402    1.8308    0.8477 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6461    1.2273    0.6386 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.1153    2.5083    1.1150 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6365    3.6015    0.2357 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9316    3.3212   -0.7489 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9560    4.9171    0.4871 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


     RDKit          2D

 75 78  0  0  0  0  0  0  0  0999 V2000
    3.7030    1.6549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9478   -4.2896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1881   -2.9741    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9286   -1.6695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6690   -0.3650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    9.1689   -0.3539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.1888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1760    3.6119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3240    3.6009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1428    1.5507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.2886    0.0578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.9300    2.9708    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.3180   -3.9128    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.4255   -2.6554    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0
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 29 30  1  0
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 31 15  1  0
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 32 73  1  1
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 32 75  1  0
M  END
> <DATABASE_ID>
NP0002830

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@]4([H])C[C@H](O)CC[C@]4(C)[C@@]3([H])C[C@H](O)[C@]12C)[C@H](C)CCC(=O)NCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H43NO5/c1-15(4-9-23(30)27-14-24(31)32)19-7-8-20-18-6-5-16-12-17(28)10-11-25(16,2)21(18)13-22(29)26(19,20)3/h15-22,28-29H,4-14H2,1-3H3,(H,27,30)(H,31,32)/t15-,16-,17-,18+,19-,20+,21+,22+,25+,26-/m1/s1

> <INCHI_KEY>
WVULKSPCQVQLCU-BUXLTGKBSA-N

> <FORMULA>
C26H43NO5

> <MOLECULAR_WEIGHT>
449.632

> <EXACT_MASS>
449.314123489

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
52.1517866816787

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(4R)-4-[(1S,2S,5R,7R,10R,11S,14R,15R,16S)-5,16-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanamido]acetic acid

> <ALOGPS_LOGP>
2.69

> <JCHEM_LOGP>
2.6859760140000004

> <ALOGPS_LOGS>
-4.76

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.837855404726056

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7733019985645173

> <JCHEM_PKA_STRONGEST_BASIC>
-0.32033464930455235

> <JCHEM_POLAR_SURFACE_AREA>
106.86000000000001

> <JCHEM_REFRACTIVITY>
122.00029999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.85e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycodeoxycholic acid

> <JCHEM_VEBER_RULE>
0

$$$$

NP0002830
     RDKit          3D

 75 78  0  0  0  0  0  0  0  0999 V2000
    3.1252   -2.9178    0.3199 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7721   -1.7217   -0.4776 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3521   -0.4197    0.0076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8450   -0.3757    0.0349 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2633    0.9542    0.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4402    1.8308    0.8477 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6461    1.2273    0.6386 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.1153    2.5083    1.1150 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6365    3.6015    0.2357 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9316    3.3212   -0.7489 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9560    4.9171    0.4871 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3965   -1.5654   -0.9448 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9537   -2.7235   -1.8691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5590   -2.6733   -1.8921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8423   -1.4304   -1.1174 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2130   -1.2286   -0.6641 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0347   -0.8209   -1.8940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4599   -0.5629   -1.5461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5101    0.5359   -0.5183 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1880    1.8358   -1.2072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4526    2.9452   -0.1821 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.3232    4.1560   -0.8303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4117    2.7537    0.9078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7281    1.4456    1.5960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6685    0.2636    0.6831 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.2872   -0.9144    1.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2552   -0.0250    0.2659 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3395   -0.3224    1.4021 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0888   -0.3088    0.8253 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1414    0.8313    0.0247 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3662   -3.6582   -1.4931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9595   -3.5884   -1.4316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9213   -2.5400   -2.9428 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.7332   -2.0956   -0.2414 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.4856    2.7881    0.1885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7871    4.8991   -0.3448 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.1338    1.3679    2.5039 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.1579   -0.5673    2.0308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5688   -1.3755    2.1286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6392   -1.7051    0.7363 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7741   -0.2631    1.6949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1386    1.6482    0.5070 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2598   -2.6886    1.8171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1491   -2.8992    0.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3425   -3.6803    0.2627 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
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  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  2 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  1
 25 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 29 31  1  0
 31 32  1  1
 31 12  1  0
 31 15  1  0
 27 16  1  0
 25 19  1  0
  1 33  1  0
  1 34  1  0
  1 35  1  0
  2 36  1  6
  3 37  1  0
  3 38  1  0
  4 39  1  0
  4 40  1  0
  7 41  1  0
  8 42  1  0
  8 43  1  0
 11 44  1  0
 12 45  1  6
 13 46  1  0
 13 47  1  0
 14 48  1  0
 14 49  1  0
 15 50  1  6
 16 51  1  1
 17 52  1  0
 17 53  1  0
 18 54  1  0
 18 55  1  0
 19 56  1  1
 20 57  1  0
 20 58  1  0
 21 59  1  1
 22 60  1  0
 23 61  1  0
 23 62  1  0
 24 63  1  0
 24 64  1  0
 26 65  1  0
 26 66  1  0
 26 67  1  0
 27 68  1  6
 28 69  1  0
 28 70  1  0
 29 71  1  1
 30 72  1  0
 32 73  1  0
 32 74  1  0
 32 75  1  0
M  END

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  C   UNK     0      30.768 -22.187   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      29.432 -22.953   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      30.788 -20.648   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      33.421 -22.140   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      28.110 -22.167   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      29.432 -24.492   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      32.124 -19.901   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      29.459 -19.875   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.775 -19.266   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      33.440 -20.680   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      26.767 -22.940   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      28.123 -20.628   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      28.097 -25.251   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      32.117 -18.356   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      29.445 -18.323   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      26.761 -24.479   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      25.438 -22.160   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      26.748 -21.394   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      33.447 -17.570   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      30.775 -16.875   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      25.438 -25.245   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      24.089 -22.940   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      34.783 -18.349   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      24.089 -24.479   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      36.112 -17.570   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      22.753 -25.238   0.000  0.00  0.00           O+0
HETATM   27  N   UNK     0      37.448 -18.349   0.000  0.00  0.00           N+0
HETATM   28  O   UNK     0      36.112 -16.031   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      38.777 -17.570   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      40.113 -18.349   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      41.443 -17.570   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      40.113 -19.888   0.000  0.00  0.00           O+0
HETATM   33  H   UNK     0      26.761 -26.062   0.000  0.00  0.00           H+0
HETATM   34  H   UNK     0      29.432 -21.369   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0      28.110 -23.750   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0      30.768 -23.770   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0      33.495 -19.109   0.000  0.00  0.00           H+0
CONECT    1    2    3    4   36                                             
CONECT    2    1    5    6   34                                             
CONECT    3    1    7    8    9                                             
CONECT    4    1   10                                                       
CONECT    5    2   11   12   35                                             
CONECT    6    2   13                                                       
CONECT    7    3   14   10   37                                             
CONECT    8    3   15   12                                                  
CONECT    9    3                                                            
CONECT   10    4    7                                                       
CONECT   11    5   16   17   18                                             
CONECT   12    5    8                                                       
CONECT   13    6   16                                                       
CONECT   14    7   19   20                                                  
CONECT   15    8                                                            
CONECT   16   11   21   13   33                                             
CONECT   17   11   22                                                       
CONECT   18   11                                                            
CONECT   19   14   23                                                       
CONECT   20   14                                                            
CONECT   21   16   24                                                       
CONECT   22   17   24                                                       
CONECT   23   19   25                                                       
CONECT   24   21   26   22                                                  
CONECT   25   23   27   28                                                  
CONECT   26   24                                                            
CONECT   27   25   29                                                       
CONECT   28   25                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   16                                                            
CONECT   34    2                                                            
CONECT   35    5                                                            
CONECT   36    1                                                            
CONECT   37    7                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

COMPND    NP0002830
HETATM    1  C1  UNL     1       3.125  -2.918   0.320  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.772  -1.722  -0.478  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.352  -0.420   0.008  1.00  0.00           C  
HETATM    4  C4  UNL     1       4.845  -0.376   0.035  1.00  0.00           C  
HETATM    5  C5  UNL     1       5.263   0.954   0.529  1.00  0.00           C  
HETATM    6  O1  UNL     1       4.440   1.831   0.848  1.00  0.00           O  
HETATM    7  N1  UNL     1       6.646   1.227   0.639  1.00  0.00           N  
HETATM    8  C6  UNL     1       7.115   2.508   1.115  1.00  0.00           C  
HETATM    9  C7  UNL     1       6.636   3.602   0.236  1.00  0.00           C  
HETATM   10  O2  UNL     1       5.932   3.321  -0.749  1.00  0.00           O  
HETATM   11  O3  UNL     1       6.956   4.917   0.487  1.00  0.00           O  
HETATM   12  C8  UNL     1       1.397  -1.565  -0.945  1.00  0.00           C  
HETATM   13  C9  UNL     1       0.954  -2.724  -1.869  1.00  0.00           C  
HETATM   14  C10 UNL     1      -0.559  -2.673  -1.892  1.00  0.00           C  
HETATM   15  C11 UNL     1      -0.842  -1.430  -1.117  1.00  0.00           C  
HETATM   16  C12 UNL     1      -2.213  -1.229  -0.664  1.00  0.00           C  
HETATM   17  C13 UNL     1      -3.035  -0.821  -1.894  1.00  0.00           C  
HETATM   18  C14 UNL     1      -4.460  -0.563  -1.546  1.00  0.00           C  
HETATM   19  C15 UNL     1      -4.510   0.536  -0.518  1.00  0.00           C  
HETATM   20  C16 UNL     1      -4.188   1.836  -1.207  1.00  0.00           C  
HETATM   21  C17 UNL     1      -4.453   2.945  -0.182  1.00  0.00           C  
HETATM   22  O4  UNL     1      -4.323   4.156  -0.830  1.00  0.00           O  
HETATM   23  C18 UNL     1      -3.412   2.754   0.908  1.00  0.00           C  
HETATM   24  C19 UNL     1      -3.728   1.446   1.596  1.00  0.00           C  
HETATM   25  C20 UNL     1      -3.668   0.264   0.683  1.00  0.00           C  
HETATM   26  C21 UNL     1      -4.287  -0.914   1.421  1.00  0.00           C  
HETATM   27  C22 UNL     1      -2.255  -0.025   0.266  1.00  0.00           C  
HETATM   28  C23 UNL     1      -1.340  -0.322   1.402  1.00  0.00           C  
HETATM   29  C24 UNL     1       0.089  -0.309   0.825  1.00  0.00           C  
HETATM   30  O5  UNL     1       0.141   0.831   0.025  1.00  0.00           O  
HETATM   31  C25 UNL     1       0.242  -1.511  -0.027  1.00  0.00           C  
HETATM   32  C26 UNL     1      -0.040  -2.779   0.732  1.00  0.00           C  
HETATM   33  H1  UNL     1       3.027  -3.818  -0.320  1.00  0.00           H  
HETATM   34  H2  UNL     1       2.592  -3.011   1.282  1.00  0.00           H  
HETATM   35  H3  UNL     1       4.209  -2.878   0.565  1.00  0.00           H  
HETATM   36  H4  UNL     1       3.369  -1.892  -1.451  1.00  0.00           H  
HETATM   37  H5  UNL     1       3.038  -0.252   1.080  1.00  0.00           H  
HETATM   38  H6  UNL     1       2.941   0.444  -0.549  1.00  0.00           H  
HETATM   39  H7  UNL     1       5.336  -0.531  -0.926  1.00  0.00           H  
HETATM   40  H8  UNL     1       5.240  -1.121   0.775  1.00  0.00           H  
HETATM   41  H9  UNL     1       7.378   0.502   0.375  1.00  0.00           H  
HETATM   42  H10 UNL     1       6.687   2.635   2.144  1.00  0.00           H  
HETATM   43  H11 UNL     1       8.206   2.541   1.162  1.00  0.00           H  
HETATM   44  H12 UNL     1       7.723   5.354   0.013  1.00  0.00           H  
HETATM   45  H13 UNL     1       1.337  -0.675  -1.608  1.00  0.00           H  
HETATM   46  H14 UNL     1       1.364  -2.511  -2.901  1.00  0.00           H  
HETATM   47  H15 UNL     1       1.366  -3.658  -1.493  1.00  0.00           H  
HETATM   48  H16 UNL     1      -0.959  -3.588  -1.432  1.00  0.00           H  
HETATM   49  H17 UNL     1      -0.921  -2.540  -2.943  1.00  0.00           H  
HETATM   50  H18 UNL     1      -0.531  -0.564  -1.753  1.00  0.00           H  
HETATM   51  H19 UNL     1      -2.733  -2.096  -0.241  1.00  0.00           H  
HETATM   52  H20 UNL     1      -2.589   0.114  -2.268  1.00  0.00           H  
HETATM   53  H21 UNL     1      -2.909  -1.583  -2.686  1.00  0.00           H  
HETATM   54  H22 UNL     1      -4.960  -0.173  -2.458  1.00  0.00           H  
HETATM   55  H23 UNL     1      -5.022  -1.468  -1.252  1.00  0.00           H  
HETATM   56  H24 UNL     1      -5.578   0.620  -0.175  1.00  0.00           H  
HETATM   57  H25 UNL     1      -3.131   1.923  -1.499  1.00  0.00           H  
HETATM   58  H26 UNL     1      -4.860   1.940  -2.070  1.00  0.00           H  
HETATM   59  H27 UNL     1      -5.486   2.788   0.188  1.00  0.00           H  
HETATM   60  H28 UNL     1      -4.787   4.899  -0.345  1.00  0.00           H  
HETATM   61  H29 UNL     1      -2.426   2.783   0.440  1.00  0.00           H  
HETATM   62  H30 UNL     1      -3.549   3.552   1.671  1.00  0.00           H  
HETATM   63  H31 UNL     1      -3.134   1.368   2.504  1.00  0.00           H  
HETATM   64  H32 UNL     1      -4.802   1.536   1.935  1.00  0.00           H  
HETATM   65  H33 UNL     1      -5.158  -0.567   2.031  1.00  0.00           H  
HETATM   66  H34 UNL     1      -3.569  -1.376   2.129  1.00  0.00           H  
HETATM   67  H35 UNL     1      -4.639  -1.705   0.736  1.00  0.00           H  
HETATM   68  H36 UNL     1      -1.881   0.838  -0.302  1.00  0.00           H  
HETATM   69  H37 UNL     1      -1.543  -1.256   1.926  1.00  0.00           H  
HETATM   70  H38 UNL     1      -1.325   0.483   2.183  1.00  0.00           H  
HETATM   71  H39 UNL     1       0.774  -0.263   1.695  1.00  0.00           H  
HETATM   72  H40 UNL     1      -0.139   1.648   0.507  1.00  0.00           H  
HETATM   73  H41 UNL     1       0.260  -2.689   1.817  1.00  0.00           H  
HETATM   74  H42 UNL     1      -1.149  -2.899   0.783  1.00  0.00           H  
HETATM   75  H43 UNL     1       0.342  -3.680   0.263  1.00  0.00           H  
CONECT    1    2   33   34   35
CONECT    2    3   12   36
CONECT    3    4   37   38
CONECT    4    5   39   40
CONECT    5    6    6    7
CONECT    7    8   41
CONECT    8    9   42   43
CONECT    9   10   10   11
CONECT   11   44
CONECT   12   13   31   45
CONECT   13   14   46   47
CONECT   14   15   48   49
CONECT   15   16   31   50
CONECT   16   17   27   51
CONECT   17   18   52   53
CONECT   18   19   54   55
CONECT   19   20   25   56
CONECT   20   21   57   58
CONECT   21   22   23   59
CONECT   22   60
CONECT   23   24   61   62
CONECT   24   25   63   64
CONECT   25   26   27
CONECT   26   65   66   67
CONECT   27   28   68
CONECT   28   29   69   70
CONECT   29   30   31   71
CONECT   30   72
CONECT   31   32
CONECT   32   73   74   75
END

NP0002830
     RDKit          3D

75 78  0  0  0  0  0  0  0  0999 V2000
    3.1252   -2.9178    0.3199 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7721   -1.7217   -0.4776 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3521   -0.4197    0.0076 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8450   -0.3757    0.0349 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2633    0.9542    0.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4402    1.8308    0.8477 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6461    1.2273    0.6386 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.1153    2.5083    1.1150 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6365    3.6015    0.2357 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9316    3.3212   -0.7489 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9560    4.9171    0.4871 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3965   -1.5654   -0.9448 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9537   -2.7235   -1.8691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5590   -2.6733   -1.8921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8423   -1.4304   -1.1174 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2130   -1.2286   -0.6641 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0347   -0.8209   -1.8940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4599   -0.5629   -1.5461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5101    0.5359   -0.5183 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1880    1.8358   -1.2072 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4526    2.9452   -0.1821 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.3232    4.1560   -0.8303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4117    2.7537    0.9078 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7281    1.4456    1.5960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6685    0.2636    0.6831 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.2872   -0.9144    1.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2552   -0.0250    0.2659 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3395   -0.3224    1.4021 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0888   -0.3088    0.8253 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1414    0.8313    0.0247 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2421   -1.5106   -0.0274 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0401   -2.7787    0.7319 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0269   -3.8182   -0.3202 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5922   -3.0108    1.2823 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2089   -2.8780    0.5645 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3687   -1.8919   -1.4511 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0384   -0.2520    1.0805 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9412    0.4438   -0.5489 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3355   -0.5315   -0.9259 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2396   -1.1208    0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3783    0.5016    0.3750 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6871    2.6346    2.1436 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2062    2.5408    1.1620 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7226    5.3542    0.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3366   -0.6751   -1.6077 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3639   -2.5111   -2.9007 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3662   -3.6582   -1.4931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9595   -3.5884   -1.4316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9213   -2.5400   -2.9428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5308   -0.5637   -1.7531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7332   -2.0956   -0.2414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5887    0.1136   -2.2683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9087   -1.5828   -2.6861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9603   -0.1726   -2.4579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0224   -1.4685   -1.2525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5782    0.6200   -0.1754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1308    1.9234   -1.4986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8603    1.9396   -2.0703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4856    2.7881    0.1885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7871    4.8991   -0.3448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4264    2.7832    0.4399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5494    3.5519    1.6713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1338    1.3679    2.5039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8024    1.5358    1.9346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1579   -0.5673    2.0308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5688   -1.3755    2.1286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6392   -1.7051    0.7363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8811    0.8380   -0.3024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5433   -1.2562    1.9257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3249    0.4828    2.1832 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7741   -0.2631    1.6949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1386    1.6482    0.5070 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2598   -2.6886    1.8171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1491   -2.8992    0.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3425   -3.6803    0.2627 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
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  2 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
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 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  1
 25 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 29 31  1  0
 31 32  1  1
 31 12  1  0
 31 15  1  0
 27 16  1  0
 25 19  1  0
  1 33  1  0
  1 34  1  0
  1 35  1  0
  2 36  1  6
  3 37  1  0
  3 38  1  0
  4 39  1  0
  4 40  1  0
  7 41  1  0
  8 42  1  0
  8 43  1  0
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 26 67  1  0
 27 68  1  6
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 28 70  1  0
 29 71  1  1
 30 72  1  0
 32 73  1  0
 32 74  1  0
 32 75  1  0
M  END

View in JSmol

Synonyms

Value	Source
Deoxycholic acid glycine conjugate	ChEBI
Deoxycholylglycine	ChEBI
GDCA	ChEBI
Glycodeoxycholate	ChEBI
Glycodesoxycholic acid	ChEBI
3alpha,12alpha-Dihydroxy-5beta-cholan-24-oylglycine	Kegg
Deoxycholate glycine conjugate	Generator
Deoxycholic acid glycine conjugic acid	Generator
Glycodesoxycholate	Generator
3a,12a-Dihydroxy-5b-cholan-24-oylglycine	Generator
3Α,12α-dihydroxy-5β-cholan-24-oylglycine	Generator
Glycodeoxycholic acid	Generator
Acid, glycodeoxycholic	MeSH
Glycine deoxycholate	MeSH
Deoxycholate, glycine	MeSH

Chemical Formula

C₂₆H₄₃NO₅

Average Mass

449.6320 Da

Monoisotopic Mass

449.31412 Da

IUPAC Name

2-[(4R)-4-[(1S,2S,5R,7R,10R,11S,14R,15R,16S)-5,16-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanamido]acetic acid

Traditional Name

glycodeoxycholic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@]4([H])C[C@H](O)CC[C@]4(C)[C@@]3([H])C[C@H](O)[C@]12C)[C@H](C)CCC(=O)NCC(O)=O

InChI Identifier

InChI=1S/C26H43NO5/c1-15(4-9-23(30)27-14-24(31)32)19-7-8-20-18-6-5-16-12-17(28)10-11-25(16,2)21(18)13-22(29)26(19,20)3/h15-22,28-29H,4-14H2,1-3H3,(H,27,30)(H,31,32)/t15-,16-,17-,18+,19-,20+,21+,22+,25+,26-/m1/s1

InChI Key

WVULKSPCQVQLCU-BUXLTGKBSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400 MHz, methanol, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, methanol, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, methanol, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces nigra	LOTUS Database	35616633
Trypanosoma brucei	LOTUS Database	35616633

Species Where Detected

Species Name	Source	Reference
Penicillium sp. SA29	KNApSAcK Database	22123792

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as glycinated bile acids and derivatives. These are compounds with a structure characterized by the presence of a glycine linked to a bile acid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Bile acids, alcohols and derivatives

Direct Parent

Glycinated bile acids and derivatives

Alternative Parents

Substituents

Glycinated bile acid
Dihydroxy bile acid, alcohol, or derivatives
Hydroxy bile acid, alcohol, or derivatives
3-hydroxysteroid
12-hydroxysteroid
Hydroxysteroid
3-alpha-hydroxysteroid
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid or derivatives
Fatty amide
Fatty acyl
N-acyl-amine
Cyclic alcohol
Carboxamide group
Secondary alcohol
Secondary carboxylic acid amide
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Alcohol
Organic nitrogen compound
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

bile acid glycine conjugate (CHEBI:27471 )
C26 bile acids, alcohols, and derivatives (C05464 )
Glycine conjugates (LMST05030006 )

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	2.69	ALOGPS
logP	2.69	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	3.77	ChemAxon
pKa (Strongest Basic)	-0.32	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	106.86 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	122 m³·mol⁻¹	ChemAxon
Polarizability	52.15 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

Not Available

KNApSAcK ID

C00030411

Chemspider ID

2299354

KEGG Compound ID

C05464

BioCyc ID

GLYCODEOXYCHOLIC_ACID

BiGG ID

Not Available

Wikipedia Link

Glycodeoxycholic_acid

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

27471

Good Scents ID

Not Available

References

General References

Khurana S, Raina H, Pappas V, Raufman JP, Pallone TL: Effects of deoxycholylglycine, a conjugated secondary bile acid, on myogenic tone and agonist-induced contraction in rat resistance arteries. PLoS One. 2012;7(2):e32006. doi: 10.1371/journal.pone.0032006. Epub 2012 Feb 16. [PubMed:22359652 ]
Cekic AB, Alhan E, Usta A, Turkyilmaz S, Kural BV, Ercin C: Effects of clotrimazol on the acute necrotizing pancreatitis in rats. Inflammation. 2013 Dec;36(6):1576-83. doi: 10.1007/s10753-013-9702-3. [PubMed:23892997 ]

Showing NP-Card for Glycodesoxycholic acid (NP0002830)

MOL for NP0002830 (Glycodesoxycholic acid)

3D MOL for NP0002830 (Glycodesoxycholic acid)

3D SDF for NP0002830 (Glycodesoxycholic acid)

3D-SDF for NP0002830 (Glycodesoxycholic acid)

PDB for NP0002830 (Glycodesoxycholic acid)

3D PDB for NP0002830 (Glycodesoxycholic acid)

SMILES for NP0002830 (Glycodesoxycholic acid)

INCHI for NP0002830 (Glycodesoxycholic acid)

Structure for NP0002830 (Glycodesoxycholic acid)

3D Structure for NP0002830 (Glycodesoxycholic acid)