MiMeDB: Showing metabocard for Violacein (MMDBc0016073)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:47:43 UTC

Update Date

2025-10-07 16:04:13 UTC

Metabolite ID

MMDBc0016073

Metabolite Identification

Common Name

Violacein

Description

Violacein is a natural pigment belonging to the class of indole-derived compounds. Its chemical structure features a complex arrangement of conjugated double bonds and heteroatoms, contributing to its vibrant violet color and various biological activities. Violacein is synthesized through the metabolic pathways of certain bacteria, notably Janthinobacterium lividum, which can convert substrates like scotta, a dairy by-product, into this compound via fermentation (PMID:41011456 ). The compound exhibits significant antimicrobial properties, as evidenced by its ability to inhibit biofilm formation, violacein production, and AHL levels in various assays (PMID:41030511 ). Additionally, violacein has been implicated in quorum sensing inhibition, as only a minority of lactic acid bacteria (LAB) isolates demonstrated the capacity to inhibit its production (PMID:41027658 ). The potential for enhancing violacein yields through optimized fermentation conditions has also been explored, achieving notable production levels in bioreactor settings (PMID:41011456 ). Overall, the chemistry of violacein, alongside its biosynthetic pathways and biological activities, underscores its significance in both microbiology and potential therapeutic applications.

Structure

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


  Mrv1652305152108472D          

 26 30  0  0  0  0            999 V2000
    6.4850    3.4294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4850    4.2544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7705    3.0169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7705    4.6669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1154   -1.9044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9359   -1.8182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9661   -0.4833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5014    1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0561    0.0154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6305   -1.2370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0561    3.4294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7865   -0.3971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0165    2.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2715    0.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2715   -1.0645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0561    4.2544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0165    1.0550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2715    3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2319    2.1349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7865    3.8419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0561   -0.8096    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2715    4.5094    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2319    1.3099    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8100   -1.3232    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.6198    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9615    3.8419    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  6  5  2  0  0  0  0
 10  5  1  0  0  0  0
 10  7  2  0  0  0  0
 11  3  1  0  0  0  0
 12  7  1  0  0  0  0
 13  8  1  0  0  0  0
 14  9  2  0  0  0  0
 14 12  1  0  0  0  0
 15  6  1  0  0  0  0
 15 12  2  0  0  0  0
 16  4  1  0  0  0  0
 16 11  1  0  0  0  0
 17  8  2  0  0  0  0
 17 14  1  0  0  0  0
 18 11  2  0  0  0  0
 18 13  1  0  0  0  0
 19 13  2  0  0  0  0
 20 18  1  0  0  0  0
 21  9  1  0  0  0  0
 21 15  1  0  0  0  0
 22 16  2  0  0  0  0
 22 20  1  0  0  0  0
 23 17  1  0  0  0  0
 23 19  1  0  0  0  0
 24 10  1  0  0  0  0
 25 19  1  0  0  0  0
 26 20  2  0  0  0  0
M  END

HMDB0259831
     RDKit          3D
Violacein
 39 43  0  0  0  0  0  0  0  0999 V2000
   -3.1918   -3.4512   -0.3532 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6258   -2.2966   -0.1535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9923   -1.8866   -0.1785 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0440   -0.6214    0.0738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1376    0.2273    0.1593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9462    1.5711    0.4467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6784    2.0768    0.6494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6088    1.2060    0.5575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7580   -0.1229    0.2765 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8732   -1.0821    0.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4184   -1.0559    0.2723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5541   -0.0903   -0.1971 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7711   -0.4192    0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8754    0.4414   -0.2739 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7652    1.6508   -0.9727 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9730    2.1721   -1.1572 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8934    1.3690   -0.6144 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2572    1.4880   -0.5553 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0198    0.5191    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3715   -0.5620    0.6224 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1010   -1.5569    1.2567 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9987   -0.6771    0.5603 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2234    0.2767   -0.0548 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6831   -1.5691    0.7599 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6164   -1.9908    0.8792 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0546   -3.1524    1.4998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1503   -0.1239    0.0081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8255    2.2156    0.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5740    3.1277    0.8706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6281    1.6140    0.7178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8824    0.8014   -0.7352 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8265    2.0896   -1.3098 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1572    3.0737   -1.6534 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7201    2.3542   -1.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0880    0.6490    0.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1075   -1.4938    1.3143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5340   -1.5181    0.9959 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4520   -2.1234    1.1470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2579   -3.1299    2.4920 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 13 24  1  0
 24 25  1  0
 25 26  1  0
 10  2  1  0
 25 11  2  0
  9  4  1  0
 23 14  1  0
 23 17  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
 12 31  1  0
 15 32  1  0
 16 33  1  0
 18 34  1  0
 19 35  1  0
 21 36  1  0
 22 37  1  0
 24 38  1  0
 26 39  1  0
M  END


  Mrv1652305152108472D          

 26 30  0  0  0  0            999 V2000
    6.4850    3.4294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4850    4.2544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7705    3.0169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7705    4.6669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1154   -1.9044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9359   -1.8182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9661   -0.4833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5014    1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0561    0.0154    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6305   -1.2370    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0561    3.4294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7865   -0.3971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0165    2.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2715    0.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2715   -1.0645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0561    4.2544    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0165    1.0550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2715    3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2319    2.1349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7865    3.8419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0561   -0.8096    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2715    4.5094    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2319    1.3099    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8100   -1.3232    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.6198    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9615    3.8419    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  6  5  2  0  0  0  0
 10  5  1  0  0  0  0
 10  7  2  0  0  0  0
 11  3  1  0  0  0  0
 12  7  1  0  0  0  0
 13  8  1  0  0  0  0
 14  9  2  0  0  0  0
 14 12  1  0  0  0  0
 15  6  1  0  0  0  0
 15 12  2  0  0  0  0
 16  4  1  0  0  0  0
 16 11  1  0  0  0  0
 17  8  2  0  0  0  0
 17 14  1  0  0  0  0
 18 11  2  0  0  0  0
 18 13  1  0  0  0  0
 19 13  2  0  0  0  0
 20 18  1  0  0  0  0
 21  9  1  0  0  0  0
 21 15  1  0  0  0  0
 22 16  2  0  0  0  0
 22 20  1  0  0  0  0
 23 17  1  0  0  0  0
 23 19  1  0  0  0  0
 24 10  1  0  0  0  0
 25 19  1  0  0  0  0
 26 20  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0016073

> <DATABASE_NAME>
MIME

> <SMILES>
OC1=C(C=C(N1)C1=CNC2=C1C=C(O)C=C2)C1=C2C=CC=CC2=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H13N3O3/c24-10-5-6-15-12(7-10)14(9-21-15)17-8-13(19(25)23-17)18-11-3-1-2-4-16(11)22-20(18)26/h1-9,21,23-25H

> <INCHI_KEY>
SHLJIZCPRXXHHZ-UHFFFAOYSA-N

> <FORMULA>
C20H13N3O3

> <MOLECULAR_WEIGHT>
343.342

> <EXACT_MASS>
343.095691291

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
35.98714720699519

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[2-hydroxy-5-(5-hydroxy-1H-indol-3-yl)-1H-pyrrol-3-yl]-2H-indol-2-one

> <ALOGPS_LOGP>
3.81

> <JCHEM_LOGP>
2.670175085666666

> <ALOGPS_LOGS>
-3.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.196757382066096

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.668738346625931

> <JCHEM_PKA_STRONGEST_BASIC>
0.05497970975744537

> <JCHEM_POLAR_SURFACE_AREA>
101.47

> <JCHEM_REFRACTIVITY>
99.45630000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.81e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[2-hydroxy-5-(5-hydroxy-1H-indol-3-yl)-1H-pyrrol-3-yl]indol-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0259831
     RDKit          3D
Violacein
 39 43  0  0  0  0  0  0  0  0999 V2000
   -3.1918   -3.4512   -0.3532 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6258   -2.2966   -0.1535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9923   -1.8866   -0.1785 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0440   -0.6214    0.0738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1376    0.2273    0.1593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9462    1.5711    0.4467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6784    2.0768    0.6494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6088    1.2060    0.5575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7580   -0.1229    0.2765 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8732   -1.0821    0.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4184   -1.0559    0.2723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5541   -0.0903   -0.1971 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7711   -0.4192    0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8754    0.4414   -0.2739 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7652    1.6508   -0.9727 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9730    2.1721   -1.1572 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8934    1.3690   -0.6144 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2572    1.4880   -0.5553 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0198    0.5191    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3715   -0.5620    0.6224 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1010   -1.5569    1.2567 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9987   -0.6771    0.5603 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2234    0.2767   -0.0548 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6831   -1.5691    0.7599 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6164   -1.9908    0.8792 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0546   -3.1524    1.4998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1503   -0.1239    0.0081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8255    2.2156    0.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5740    3.1277    0.8706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6281    1.6140    0.7178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8824    0.8014   -0.7352 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8265    2.0896   -1.3098 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1572    3.0737   -1.6534 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7201    2.3542   -1.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0880    0.6490    0.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1075   -1.4938    1.3143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5340   -1.5181    0.9959 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4520   -2.1234    1.1470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2579   -3.1299    2.4920 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 13 24  1  0
 24 25  1  0
 25 26  1  0
 10  2  1  0
 25 11  2  0
  9  4  1  0
 23 14  1  0
 23 17  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
 12 31  1  0
 15 32  1  0
 16 33  1  0
 18 34  1  0
 19 35  1  0
 21 36  1  0
 22 37  1  0
 24 38  1  0
 26 39  1  0
M  END

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      12.105   6.402   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.105   7.942   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.772   5.632   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.772   8.712   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.815  -3.555   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.347  -3.394   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.537  -0.902   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.403   3.215   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.438   0.029   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.910  -2.309   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.438   6.402   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.068  -0.741   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.497   4.461   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.973   0.505   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.973  -1.987   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.438   7.942   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.497   1.969   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.973   5.926   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.033   3.985   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.068   7.172   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       9.438  -1.511   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       7.973   8.417   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0       6.033   2.445   0.000  0.00  0.00           N+0
HETATM   24  O   UNK     0       3.379  -2.470   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       4.787   4.890   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       5.528   7.172   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1   11                                                       
CONECT    4    2   16                                                       
CONECT    5    6   10                                                       
CONECT    6    5   15                                                       
CONECT    7   10   12                                                       
CONECT    8   13   17                                                       
CONECT    9   14   21                                                       
CONECT   10    5    7   24                                                  
CONECT   11    3   16   18                                                  
CONECT   12    7   14   15                                                  
CONECT   13    8   18   19                                                  
CONECT   14    9   12   17                                                  
CONECT   15    6   12   21                                                  
CONECT   16    4   11   22                                                  
CONECT   17    8   14   23                                                  
CONECT   18   11   13   20                                                  
CONECT   19   13   23   25                                                  
CONECT   20   18   22   26                                                  
CONECT   21    9   15                                                       
CONECT   22   16   20                                                       
CONECT   23   17   19                                                       
CONECT   24   10                                                            
CONECT   25   19                                                            
CONECT   26   20                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   60    0
END

COMPND    HMDB0259831
HETATM    1  O1  UNL     1      -3.192  -3.451  -0.353  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.626  -2.297  -0.154  1.00  0.00           C  
HETATM    3  N1  UNL     1      -4.992  -1.887  -0.179  1.00  0.00           N  
HETATM    4  C2  UNL     1      -5.044  -0.621   0.074  1.00  0.00           C  
HETATM    5  C3  UNL     1      -6.138   0.227   0.159  1.00  0.00           C  
HETATM    6  C4  UNL     1      -5.946   1.571   0.447  1.00  0.00           C  
HETATM    7  C5  UNL     1      -4.678   2.077   0.649  1.00  0.00           C  
HETATM    8  C6  UNL     1      -3.609   1.206   0.558  1.00  0.00           C  
HETATM    9  C7  UNL     1      -3.758  -0.123   0.276  1.00  0.00           C  
HETATM   10  C8  UNL     1      -2.873  -1.082   0.152  1.00  0.00           C  
HETATM   11  C9  UNL     1      -1.418  -1.056   0.272  1.00  0.00           C  
HETATM   12  C10 UNL     1      -0.554  -0.090  -0.197  1.00  0.00           C  
HETATM   13  C11 UNL     1       0.771  -0.419   0.113  1.00  0.00           C  
HETATM   14  C12 UNL     1       1.875   0.441  -0.274  1.00  0.00           C  
HETATM   15  C13 UNL     1       1.765   1.651  -0.973  1.00  0.00           C  
HETATM   16  N2  UNL     1       2.973   2.172  -1.157  1.00  0.00           N  
HETATM   17  C14 UNL     1       3.893   1.369  -0.614  1.00  0.00           C  
HETATM   18  C15 UNL     1       5.257   1.488  -0.555  1.00  0.00           C  
HETATM   19  C16 UNL     1       6.020   0.519   0.067  1.00  0.00           C  
HETATM   20  C17 UNL     1       5.372  -0.562   0.622  1.00  0.00           C  
HETATM   21  O2  UNL     1       6.101  -1.557   1.257  1.00  0.00           O  
HETATM   22  C18 UNL     1       3.999  -0.677   0.560  1.00  0.00           C  
HETATM   23  C19 UNL     1       3.223   0.277  -0.055  1.00  0.00           C  
HETATM   24  N3  UNL     1       0.683  -1.569   0.760  1.00  0.00           N  
HETATM   25  C20 UNL     1      -0.616  -1.991   0.879  1.00  0.00           C  
HETATM   26  O3  UNL     1      -1.055  -3.152   1.500  1.00  0.00           O  
HETATM   27  H1  UNL     1      -7.150  -0.124   0.008  1.00  0.00           H  
HETATM   28  H2  UNL     1      -6.826   2.216   0.508  1.00  0.00           H  
HETATM   29  H3  UNL     1      -4.574   3.128   0.871  1.00  0.00           H  
HETATM   30  H4  UNL     1      -2.628   1.614   0.718  1.00  0.00           H  
HETATM   31  H5  UNL     1      -0.882   0.801  -0.735  1.00  0.00           H  
HETATM   32  H6  UNL     1       0.826   2.090  -1.310  1.00  0.00           H  
HETATM   33  H7  UNL     1       3.157   3.074  -1.653  1.00  0.00           H  
HETATM   34  H8  UNL     1       5.720   2.354  -1.005  1.00  0.00           H  
HETATM   35  H9  UNL     1       7.088   0.649   0.093  1.00  0.00           H  
HETATM   36  H10 UNL     1       7.107  -1.494   1.314  1.00  0.00           H  
HETATM   37  H11 UNL     1       3.534  -1.518   0.996  1.00  0.00           H  
HETATM   38  H12 UNL     1       1.452  -2.123   1.147  1.00  0.00           H  
HETATM   39  H13 UNL     1      -1.258  -3.130   2.492  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4    4
CONECT    4    5    9
CONECT    5    6    6   27
CONECT    6    7   28
CONECT    7    8    8   29
CONECT    8    9   30
CONECT    9   10   10
CONECT   10   11
CONECT   11   12   25   25
CONECT   12   13   13   31
CONECT   13   14   24
CONECT   14   15   15   23
CONECT   15   16   32
CONECT   16   17   33
CONECT   17   18   18   23
CONECT   18   19   34
CONECT   19   20   20   35
CONECT   20   21   22
CONECT   21   36
CONECT   22   23   23   37
CONECT   24   25   38
CONECT   25   26
CONECT   26   39
END

HMDB0259831
     RDKit          3D
Violacein
 39 43  0  0  0  0  0  0  0  0999 V2000
   -3.1918   -3.4512   -0.3532 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6258   -2.2966   -0.1535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9923   -1.8866   -0.1785 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0440   -0.6214    0.0738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1376    0.2273    0.1593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9462    1.5711    0.4467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6784    2.0768    0.6494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6088    1.2060    0.5575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7580   -0.1229    0.2765 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8732   -1.0821    0.1520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4184   -1.0559    0.2723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5541   -0.0903   -0.1971 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7711   -0.4192    0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8754    0.4414   -0.2739 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7652    1.6508   -0.9727 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9730    2.1721   -1.1572 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8934    1.3690   -0.6144 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2572    1.4880   -0.5553 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0198    0.5191    0.0672 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3715   -0.5620    0.6224 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1010   -1.5569    1.2567 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9987   -0.6771    0.5603 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2234    0.2767   -0.0548 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6831   -1.5691    0.7599 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6164   -1.9908    0.8792 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0546   -3.1524    1.4998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1503   -0.1239    0.0081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8255    2.2156    0.5078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5740    3.1277    0.8706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6281    1.6140    0.7178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8824    0.8014   -0.7352 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8265    2.0896   -1.3098 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1572    3.0737   -1.6534 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7201    2.3542   -1.0054 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0880    0.6490    0.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1075   -1.4938    1.3143 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5340   -1.5181    0.9959 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4520   -2.1234    1.1470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2579   -3.1299    2.4920 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 20 22  1  0
 22 23  2  0
 13 24  1  0
 24 25  1  0
 25 26  1  0
 10  2  1  0
 25 11  2  0
  9  4  1  0
 23 14  1  0
 23 17  1  0
  5 27  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
 12 31  1  0
 15 32  1  0
 16 33  1  0
 18 34  1  0
 19 35  1  0
 21 36  1  0
 22 37  1  0
 24 38  1  0
 26 39  1  0
M  END

Synonyms

Value	Source
3-(1,2-Dihydro-5-(5-hydroxy-1H-indole-3-yl)-2-oxo-3H-pyrrol-3-ylidene)-1,3-dihydro-2H-indole-2-one	HMDB
(3E)-3-(1,2-Dihydro-5-(5-hydroxy-1H-indol-3-yl)-2-oxo-3H-pyrrol-3-ylidene)-1,3-dihydro-2H-indol-2-one	HMDB

Molecular Formula

C₂₀H₁₃N₃O₃

Average Mass

343.342

Monoisotopic Mass

343.095691291

IUPAC Name

3-[2-hydroxy-5-(5-hydroxy-1H-indol-3-yl)-1H-pyrrol-3-yl]-2H-indol-2-one

Traditional Name

3-[2-hydroxy-5-(5-hydroxy-1H-indol-3-yl)-1H-pyrrol-3-yl]indol-2-one

CAS Registry Number

Not Available

SMILES

OC1=C(C=C(N1)C1=CNC2=C1C=C(O)C=C2)C1=C2C=CC=CC2=NC1=O

InChI Identifier

InChI=1S/C20H13N3O3/c24-10-5-6-15-12(7-10)14(9-21-15)17-8-13(19(25)23-17)18-11-3-1-2-4-16(11)22-20(18)26/h1-9,21,23-25H

InChI Key

SHLJIZCPRXXHHZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxyindoles. These are organic compounds containing an indole moiety that carries a hydroxyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Hydroxyindoles

Direct Parent

Hydroxyindoles

Alternative Parents

Substituents

Hydroxyindole
Indole
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
N-acylimine
Azacycle
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.038 g/L	ALOGPS
logP	3.81	ALOGPS
logP	2.67	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	7.67	ChemAxon
pKa (Strongest Basic)	0.055	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	101.47 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	99.46 m³·mol⁻¹	ChemAxon
Polarizability	35.99 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-02t9-0209000000-889cafac2f91db93ed8e	2021-09-24	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_6) - 70eV, Positive	Not Available	2021-11-05	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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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
Bacteria/Eubacteria	Proteobacteria	1		Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

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

External Links

HMDB ID

HMDB0259831

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00029223

Chemspider ID

78435916

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Violacein

METLIN ID

Not Available

PubChem Compound

11053

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

SHLJIZCPRXXHHZ-UHFFFAOYSA-N

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Violacein (MMDBc0016073)

MOL for #<Metabolite:0x00007f8d9402a480>

3D MOL for #<Metabolite:0x00007f8d9402a480>

3D SDF for #<Metabolite:0x00007f8d9402a480>

3D-SDF for #<Metabolite:0x00007f8d9402a480>

PDB for #<Metabolite:0x00007f8d9402a480>

3D PDB for #<Metabolite:0x00007f8d9402a480>

SMILES for #<Metabolite:0x00007f8d9402a480>

INCHI for #<Metabolite:0x00007f8d9402a480>

Structure for #<Metabolite:0x00007f8d9402a480>

3D Structure for #<Metabolite:0x00007f8d9402a480>