MiMeDB: Showing metabocard for Apicidin F (MMDBc0009030)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 01:41:09 UTC

Update Date

2022-08-31 06:29:29 UTC

Metabolite ID

MMDBc0009030

Metabolite Identification

Common Name

Apicidin F

Description

apicidin F 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. apicidin F is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152103412D          

 51 55  0  0  1  0            999 V2000
   -1.0069   -6.5571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9849   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9849   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2704   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1167   -6.3235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5036   -6.8755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2704   -2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5559   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9452   -5.5165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7190   -6.6206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -3.7934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0045   -4.5941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5559   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -4.5079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1606   -5.2616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250   -3.0789    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1270   -1.9520    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5475   -5.8136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2388   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.0789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -2.3645    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.3645    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1670   -5.4011    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9533   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2388   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -3.7934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9207   -5.7366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -3.0789    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -2.7770    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  3  1  0  0  0  0
  9  8  2  0  0  0  0
 11 10  1  0  0  0  0
 12  4  1  0  0  0  0
 13  5  2  0  0  0  0
 14  8  1  0  0  0  0
 15  6  1  0  0  0  0
 16  9  1  0  0  0  0
 17 10  1  0  0  0  0
 18  7  1  0  0  0  0
 19 11  1  0  0  0  0
 23 12  2  0  0  0  0
 23 13  1  0  0  0  0
 23 20  1  0  0  0  0
 24 21  1  0  0  0  0
 24 22  2  0  0  0  0
 25 14  2  0  0  0  0
 25 24  1  0  0  0  0
 26 15  1  1  0  0  0
 27 21  1  1  0  0  0
 28 20  1  1  0  0  0
 29 16  2  0  0  0  0
 29 25  1  0  0  0  0
 30 17  1  0  0  0  0
 31 18  1  0  0  0  0
 32 26  1  0  0  0  0
 33 27  1  0  0  0  0
 34 30  1  0  0  0  0
 35 28  1  0  0  0  0
 36 26  1  0  0  0  0
 36 34  2  0  0  0  0
 37 27  1  0  0  0  0
 37 32  2  0  0  0  0
 38 28  1  0  0  0  0
 38 33  2  0  0  0  0
 39 19  1  0  0  0  0
 39 30  1  0  0  0  0
 39 35  1  0  0  0  0
 40 22  1  0  0  0  0
 40 29  1  0  0  0  0
 41 31  2  0  0  0  0
 42 31  1  0  0  0  0
 32 43  1  4  0  0  0
 33 44  1  4  0  0  0
 34 45  1  4  0  0  0
 46 35  2  0  0  0  0
 47  1  1  0  0  0  0
 47 40  1  0  0  0  0
 26 48  1  6  0  0  0
 27 49  1  6  0  0  0
 28 50  1  6  0  0  0
 30 51  1  1  0  0  0
M  END


  Mrv1652305152103412D          

 51 55  0  0  1  0            999 V2000
   -1.0069   -6.5571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9849   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9849   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2704   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1167   -6.3235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5036   -6.8755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2704   -2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5559   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9452   -5.5165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7190   -6.6206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -3.7934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0045   -4.5941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5559   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -4.5079    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1606   -5.2616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250   -3.0789    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1270   -1.9520    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5475   -5.8136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2388   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520   -1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.0789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -2.3645    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -2.3645    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1670   -5.4011    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9533   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2388   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -3.7934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9207   -5.7366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -3.0789    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -2.7770    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  3  1  0  0  0  0
  9  8  2  0  0  0  0
 11 10  1  0  0  0  0
 12  4  1  0  0  0  0
 13  5  2  0  0  0  0
 14  8  1  0  0  0  0
 15  6  1  0  0  0  0
 16  9  1  0  0  0  0
 17 10  1  0  0  0  0
 18  7  1  0  0  0  0
 19 11  1  0  0  0  0
 23 12  2  0  0  0  0
 23 13  1  0  0  0  0
 23 20  1  0  0  0  0
 24 21  1  0  0  0  0
 24 22  2  0  0  0  0
 25 14  2  0  0  0  0
 25 24  1  0  0  0  0
 26 15  1  1  0  0  0
 27 21  1  1  0  0  0
 28 20  1  1  0  0  0
 29 16  2  0  0  0  0
 29 25  1  0  0  0  0
 30 17  1  0  0  0  0
 31 18  1  0  0  0  0
 32 26  1  0  0  0  0
 33 27  1  0  0  0  0
 34 30  1  0  0  0  0
 35 28  1  0  0  0  0
 36 26  1  0  0  0  0
 36 34  2  0  0  0  0
 37 27  1  0  0  0  0
 37 32  2  0  0  0  0
 38 28  1  0  0  0  0
 38 33  2  0  0  0  0
 39 19  1  0  0  0  0
 39 30  1  0  0  0  0
 39 35  1  0  0  0  0
 40 22  1  0  0  0  0
 40 29  1  0  0  0  0
 41 31  2  0  0  0  0
 42 31  1  0  0  0  0
 32 43  1  4  0  0  0
 33 44  1  4  0  0  0
 34 45  1  4  0  0  0
 46 35  2  0  0  0  0
 47  1  1  0  0  0  0
 47 40  1  0  0  0  0
 26 48  1  6  0  0  0
 27 49  1  6  0  0  0
 28 50  1  6  0  0  0
 30 51  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009030

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12CCCCN1C(=O)[C@]([H])(CC1=CC=CC=C1)N=C(O)[C@]([H])(CC1=CN(OC)C3=CC=CC=C13)N=C(O)[C@]([H])(CCCCCC(O)=O)N=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C35H43N5O7/c1-47-40-22-24(25-14-8-9-16-29(25)40)21-27-33(44)38-28(20-23-12-4-2-5-13-23)35(46)39-19-11-10-17-30(39)34(45)36-26(32(43)37-27)15-6-3-7-18-31(41)42/h2,4-5,8-9,12-14,16,22,26-28,30H,3,6-7,10-11,15,17-21H2,1H3,(H,36,45)(H,37,43)(H,38,44)(H,41,42)/t26-,27-,28-,30+/m0/s1

> <INCHI_KEY>
NTAHFSRRNUUVIN-VNDOHOEKSA-N

> <FORMULA>
C35H43N5O7

> <MOLECULAR_WEIGHT>
645.757

> <EXACT_MASS>
645.316248745

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
90

> <JCHEM_AVERAGE_POLARIZABILITY>
68.31058655644705

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[(3S,6S,9S,15aR)-9-benzyl-1,4,7-trihydroxy-6-[(1-methoxy-1H-indol-3-yl)methyl]-10-oxo-3H,6H,9H,10H,12H,13H,14H,15H,15aH-pyrido[1,2-a]1,4,7,10-tetraazacyclododecan-3-yl]hexanoic acid

> <ALOGPS_LOGP>
2.99

> <JCHEM_LOGP>
3.3415805479102705

> <ALOGPS_LOGS>
-4.07

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.8165834487741286

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.8338287354932161

> <JCHEM_PKA_STRONGEST_BASIC>
5.4996751814023925

> <JCHEM_POLAR_SURFACE_AREA>
169.54

> <JCHEM_REFRACTIVITY>
175.62030000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.44e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-[(3S,6S,9S,15aR)-9-benzyl-1,4,7-trihydroxy-6-[(1-methoxyindol-3-yl)methyl]-10-oxo-3H,6H,9H,12H,13H,14H,15H,15aH-pyrido[1,2-a]1,4,7,10-tetraazacyclododecan-3-yl]hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -1.880 -12.240   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -7.438  -2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.645  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -7.438  -3.644   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.105  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.311  -2.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.978  -2.104   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.951 -11.804   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.807 -12.834   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.310   1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.080   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.105  -4.414   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.771  -2.104   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.631 -10.297   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.977  -1.334   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.342 -12.358   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.312  -1.334   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.437  -4.414   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.310  -7.081   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.008  -8.576   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -4.771  -3.644   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.540  -8.415   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.166  -9.822   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.644  -2.104   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.540  -5.747   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.104  -3.644   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.022 -10.852   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      11.646  -2.104   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.644  -3.644   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       0.000  -5.747   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -2.104  -2.104   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0       2.310  -1.334   0.000  0.00  0.00           N+0
HETATM   37  N   UNK     0       2.310  -4.414   0.000  0.00  0.00           N+0
HETATM   38  N   UNK     0      -0.770  -4.414   0.000  0.00  0.00           N+0
HETATM   39  N   UNK     0      -0.770  -1.334   0.000  0.00  0.00           N+0
HETATM   40  N   UNK     0      -0.312 -10.082   0.000  0.00  0.00           N+0
HETATM   41  O   UNK     0      12.979  -1.334   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      11.646  -3.644   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       4.977  -4.414   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      -0.770  -7.081   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0       2.310   1.334   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      -3.437  -1.334   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      -1.719 -10.708   0.000  0.00  0.00           O+0
HETATM   48  H   UNK     0       4.977  -2.874   0.000  0.00  0.00           H+0
HETATM   49  H   UNK     0       3.080  -5.747   0.000  0.00  0.00           H+0
HETATM   50  H   UNK     0      -2.104  -5.184   0.000  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.770  -1.334   0.000  0.00  0.00           H+0
CONECT    1   47                                                            
CONECT    2    4    5                                                       
CONECT    3    6    7                                                       
CONECT    4    2   12                                                       
CONECT    5    2   13                                                       
CONECT    6    3   15                                                       
CONECT    7    3   18                                                       
CONECT    8    9   14                                                       
CONECT    9    8   16                                                       
CONECT   10   11   17                                                       
CONECT   11   10   19                                                       
CONECT   12    4   23                                                       
CONECT   13    5   23                                                       
CONECT   14    8   25                                                       
CONECT   15    6   26                                                       
CONECT   16    9   29                                                       
CONECT   17   10   30                                                       
CONECT   18    7   31                                                       
CONECT   19   11   39                                                       
CONECT   20   23   28                                                       
CONECT   21   24   27                                                       
CONECT   22   24   40                                                       
CONECT   23   12   13   20                                                  
CONECT   24   21   22   25                                                  
CONECT   25   14   24   29                                                  
CONECT   26   15   32   36   48                                             
CONECT   27   21   33   37   49                                             
CONECT   28   20   35   38   50                                             
CONECT   29   16   25   40                                                  
CONECT   30   17   34   39   51                                             
CONECT   31   18   41   42                                                  
CONECT   32   26   37   43                                                  
CONECT   33   27   38   44                                                  
CONECT   34   30   36   45                                                  
CONECT   35   28   39   46                                                  
CONECT   36   26   34                                                       
CONECT   37   27   32                                                       
CONECT   38   28   33                                                       
CONECT   39   19   30   35                                                  
CONECT   40   22   29   47                                                  
CONECT   41   31                                                            
CONECT   42   31                                                            
CONECT   43   32                                                            
CONECT   44   33                                                            
CONECT   45   34                                                            
CONECT   46   35                                                            
CONECT   47    1   40                                                       
CONECT   48   26                                                            
CONECT   49   27                                                            
CONECT   50   28                                                            
CONECT   51   30                                                            
MASTER        0    0    0    0    0    0    0    0   51    0  110    0
END

Synonyms

Not Available

Molecular Formula

C₃₅H₄₃N₅O₇

Average Mass

645.757

Monoisotopic Mass

645.316248745

IUPAC Name

6-[(3S,6S,9S,15aR)-9-benzyl-1,4,7-trihydroxy-6-[(1-methoxy-1H-indol-3-yl)methyl]-10-oxo-3H,6H,9H,10H,12H,13H,14H,15H,15aH-pyrido[1,2-a]1,4,7,10-tetraazacyclododecan-3-yl]hexanoic acid

Traditional Name

6-[(3S,6S,9S,15aR)-9-benzyl-1,4,7-trihydroxy-6-[(1-methoxyindol-3-yl)methyl]-10-oxo-3H,6H,9H,12H,13H,14H,15H,15aH-pyrido[1,2-a]1,4,7,10-tetraazacyclododecan-3-yl]hexanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@]12CCCCN1C(=O)[C@]([H])(CC1=CC=CC=C1)N=C(O)[C@]([H])(CC1=CN(OC)C3=CC=CC=C13)N=C(O)[C@]([H])(CCCCCC(O)=O)N=C2O

InChI Identifier

InChI=1S/C35H43N5O7/c1-47-40-22-24(25-14-8-9-16-29(25)40)21-27-33(44)38-28(20-23-12-4-2-5-13-23)35(46)39-19-11-10-17-30(39)34(45)36-26(32(43)37-27)15-6-3-7-18-31(41)42/h2,4-5,8-9,12-14,16,22,26-28,30H,3,6-7,10-11,15,17-21H2,1H3,(H,36,45)(H,37,43)(H,38,44)(H,41,42)/t26-,27-,28-,30+/m0/s1

InChI Key

NTAHFSRRNUUVIN-VNDOHOEKSA-N

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
Macrolactam
Alpha-amino acid or derivatives
3-alkylindole
Indole
Indole or derivatives
Medium-chain fatty acid
Amino fatty acid
Heterocyclic fatty acid
Monocyclic benzene moiety
Fatty acyl
Piperidine
Substituted pyrrole
Fatty acid
Benzenoid
Pyrrole
Tertiary carboxylic acid amide
Heteroaromatic compound
Carboxamide group
Secondary carboxylic acid amide
Lactam
Organoheterocyclic compound
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Organic oxide
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.054 g/L	ALOGPS
logP	2.99	ALOGPS
logP	3.34	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	-0.83	ChemAxon
pKa (Strongest Basic)	5.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	169.54 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	175.62 m³·mol⁻¹	ChemAxon
Polarizability	68.31 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

31142541

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

72945291

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Apicidin F (MMDBc0009030)

MOL for #<Metabolite:0x00007fdb20bdfdf0>

3D MOL for #<Metabolite:0x00007fdb20bdfdf0>

3D SDF for #<Metabolite:0x00007fdb20bdfdf0>

3D-SDF for #<Metabolite:0x00007fdb20bdfdf0>

PDB for #<Metabolite:0x00007fdb20bdfdf0>

3D PDB for #<Metabolite:0x00007fdb20bdfdf0>

SMILES for #<Metabolite:0x00007fdb20bdfdf0>

INCHI for #<Metabolite:0x00007fdb20bdfdf0>

Structure for #<Metabolite:0x00007fdb20bdfdf0>

3D Structure for #<Metabolite:0x00007fdb20bdfdf0>