MiMeDB: Showing metabocard for Vulnibactin 3 (MMDBc0019048)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 09:10:18 UTC

Update Date

2022-08-31 06:44:50 UTC

Metabolite ID

MMDBc0019048

Metabolite Identification

Common Name

Vulnibactin 3

Description

Vulnibactin 3 belongs to the class of organic compounds known as salicylamides. These are carboxamide derivatives of salicylic acid. Salicylic acid is the ortho-hydroxylated derivative of benzoic acid. Vulnibactin 3 is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152111102D          

 34 36  0  0  0  0            999 V2000
    2.6472   -4.8550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4930   -0.5457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6725   -0.4595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8285   -1.2994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1876   -1.1269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8187   -4.0481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3436   -1.9668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5231   -1.8806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6791   -2.7205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4861   -2.8920    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0382   -2.5480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2666   -3.4350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  7  2  1  0  0  0  0
  8  4  2  0  0  0  0
  9  3  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  5  1  0  0  0  0
 14  6  1  0  0  0  0
 15  1  1  0  0  0  0
 16  7  2  0  0  0  0
 17  8  1  0  0  0  0
 18  9  2  0  0  0  0
 18 16  1  0  0  0  0
 19 10  2  0  0  0  0
 20 15  1  0  0  0  0
 21 17  2  0  0  0  0
 21 19  1  0  0  0  0
 22 17  1  0  0  0  0
 23 20  1  0  0  0  0
 24 16  1  0  0  0  0
 25 11  1  0  0  0  0
 25 12  1  0  0  0  0
 26 13  1  4  0  0  0
 26 22  2  0  0  0  0
 27 14  1  4  0  0  0
 27 23  2  0  0  0  0
 28 20  1  0  0  0  0
 28 24  2  0  0  0  0
 29 18  1  0  0  0  0
 30 19  1  0  0  0  0
 31 21  1  0  0  0  0
 32 22  1  0  0  0  0
 33 23  1  0  0  0  0
 34 15  1  0  0  0  0
 34 24  1  0  0  0  0
M  END


  Mrv1652305152111102D          

 34 36  0  0  0  0            999 V2000
    2.6472   -4.8550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4930   -0.5457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6725   -0.4595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8285   -1.2994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1876   -1.1269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8187   -4.0481    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3436   -1.9668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5231   -1.8806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6791   -2.7205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4861   -2.8920    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0382   -2.5480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2666   -3.4350    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  7  2  1  0  0  0  0
  8  4  2  0  0  0  0
  9  3  1  0  0  0  0
 10  4  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  5  1  0  0  0  0
 14  6  1  0  0  0  0
 15  1  1  0  0  0  0
 16  7  2  0  0  0  0
 17  8  1  0  0  0  0
 18  9  2  0  0  0  0
 18 16  1  0  0  0  0
 19 10  2  0  0  0  0
 20 15  1  0  0  0  0
 21 17  2  0  0  0  0
 21 19  1  0  0  0  0
 22 17  1  0  0  0  0
 23 20  1  0  0  0  0
 24 16  1  0  0  0  0
 25 11  1  0  0  0  0
 25 12  1  0  0  0  0
 26 13  1  4  0  0  0
 26 22  2  0  0  0  0
 27 14  1  4  0  0  0
 27 23  2  0  0  0  0
 28 20  1  0  0  0  0
 28 24  2  0  0  0  0
 29 18  1  0  0  0  0
 30 19  1  0  0  0  0
 31 21  1  0  0  0  0
 32 22  1  0  0  0  0
 33 23  1  0  0  0  0
 34 15  1  0  0  0  0
 34 24  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0019048

> <DATABASE_NAME>
MIME

> <SMILES>
CC1OC(=NC1C(O)=NCCCNCCCN=C(O)C1=C(O)C(O)=CC=C1)C1=CC=CC=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H30N4O6/c1-15-20(28-24(34-15)16-7-2-3-9-18(16)29)23(33)27-14-6-12-25-11-5-13-26-22(32)17-8-4-10-19(30)21(17)31/h2-4,7-10,15,20,25,29-31H,5-6,11-14H2,1H3,(H,26,32)(H,27,33)

> <INCHI_KEY>
OPCNBYUJAGAASS-UHFFFAOYSA-N

> <FORMULA>
C24H30N4O6

> <MOLECULAR_WEIGHT>
470.526

> <EXACT_MASS>
470.216534702

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
52.00536430460523

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydroxy-N-(3-{[3-({hydroxy[2-(2-hydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazol-4-yl]methylidene}amino)propyl]amino}propyl)benzene-1-carboximidic acid

> <ALOGPS_LOGP>
2.07

> <JCHEM_LOGP>
-1.132842611777951

> <ALOGPS_LOGS>
-3.90

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
7.493220468628413

> <JCHEM_PKA_STRONGEST_ACIDIC>
-4.829555819266859

> <JCHEM_PKA_STRONGEST_BASIC>
11.785731322180224

> <JCHEM_POLAR_SURFACE_AREA>
159.48999999999998

> <JCHEM_REFRACTIVITY>
127.80999999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.99e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxy-N-(3-{[3-({hydroxy[2-(2-hydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazol-4-yl]methylidene}amino)propyl]amino}propyl)benzenecarboximidic 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       4.941  -9.063   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.654  -1.019   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.122  -0.858   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      22.673  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.004  -9.240   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.280  -2.426   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      21.339  -7.700   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.217  -2.104   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      24.006  -7.700   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.670 -10.010   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      17.338 -10.010   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.262  -7.556   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.375  -3.671   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      21.339  -9.240   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.843  -3.510   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      24.006  -9.240   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      22.673 -10.010   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      20.005 -10.010   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.001  -5.078   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0      13.337  -9.240   0.000  0.00  0.00           N+0
HETATM   26  N   UNK     0      18.672  -9.240   0.000  0.00  0.00           N+0
HETATM   27  N   UNK     0       8.002  -9.240   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0       6.507  -5.398   0.000  0.00  0.00           N+0
HETATM   29  O   UNK     0       1.938  -4.756   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      25.340 -10.010   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      22.673 -11.550   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      20.005 -11.550   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       4.231  -6.412   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2    3    7                                                       
CONECT    3    2    9                                                       
CONECT    4    8   10                                                       
CONECT    5   11   13                                                       
CONECT    6   12   14                                                       
CONECT    7    2   16                                                       
CONECT    8    4   17                                                       
CONECT    9    3   18                                                       
CONECT   10    4   19                                                       
CONECT   11    5   25                                                       
CONECT   12    6   25                                                       
CONECT   13    5   26                                                       
CONECT   14    6   27                                                       
CONECT   15    1   20   34                                                  
CONECT   16    7   18   24                                                  
CONECT   17    8   21   22                                                  
CONECT   18    9   16   29                                                  
CONECT   19   10   21   30                                                  
CONECT   20   15   23   28                                                  
CONECT   21   17   19   31                                                  
CONECT   22   17   26   32                                                  
CONECT   23   20   27   33                                                  
CONECT   24   16   28   34                                                  
CONECT   25   11   12                                                       
CONECT   26   13   22                                                       
CONECT   27   14   23                                                       
CONECT   28   20   24                                                       
CONECT   29   18                                                            
CONECT   30   19                                                            
CONECT   31   21                                                            
CONECT   32   22                                                            
CONECT   33   23                                                            
CONECT   34   15   24                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

Synonyms

Not Available

Molecular Formula

C₂₄H₃₀N₄O₆

Average Mass

470.526

Monoisotopic Mass

470.216534702

IUPAC Name

2,3-dihydroxy-N-(3-{[3-({hydroxy[2-(2-hydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazol-4-yl]methylidene}amino)propyl]amino}propyl)benzene-1-carboximidic acid

Traditional Name

2,3-dihydroxy-N-(3-{[3-({hydroxy[2-(2-hydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazol-4-yl]methylidene}amino)propyl]amino}propyl)benzenecarboximidic acid

CAS Registry Number

Not Available

SMILES

CC1OC(=NC1C(O)=NCCCNCCCN=C(O)C1=C(O)C(O)=CC=C1)C1=CC=CC=C1O

InChI Identifier

InChI=1S/C24H30N4O6/c1-15-20(28-24(34-15)16-7-2-3-9-18(16)29)23(33)27-14-6-12-25-11-5-13-26-22(32)17-8-4-10-19(30)21(17)31/h2-4,7-10,15,20,25,29-31H,5-6,11-14H2,1H3,(H,26,32)(H,27,33)

InChI Key

OPCNBYUJAGAASS-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as salicylamides. These are carboxamide derivatives of salicylic acid. Salicylic acid is the ortho-hydroxylated derivative of benzoic acid.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Salicylamides

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Salicylamide
Benzamide
Benzoyl
Catechol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Oxazoline
Vinylogous acid
Amino acid or derivatives
Carboxamide group
Secondary carboxylic acid amide
Organoheterocyclic compound
Secondary amine
Azacycle
Oxacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboxylic acid derivative
Secondary aliphatic amine
Organic nitrogen compound
Organic oxide
Organonitrogen compound
Amine
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.06 g/L	ALOGPS
logP	2.07	ALOGPS
logP	-1.1	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	-4.8	ChemAxon
pKa (Strongest Basic)	11.79	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	159.49 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	127.81 m³·mol⁻¹	ChemAxon
Polarizability	52.01 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

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
Bacteria	Proteobacteria	1	Human	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78435113

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139588390

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 Vulnibactin 3 (MMDBc0019048)

MOL for #<Metabolite:0x00007fecad12db20>

3D MOL for #<Metabolite:0x00007fecad12db20>

3D SDF for #<Metabolite:0x00007fecad12db20>

3D-SDF for #<Metabolite:0x00007fecad12db20>

PDB for #<Metabolite:0x00007fecad12db20>

3D PDB for #<Metabolite:0x00007fecad12db20>

SMILES for #<Metabolite:0x00007fecad12db20>

INCHI for #<Metabolite:0x00007fecad12db20>

Structure for #<Metabolite:0x00007fecad12db20>

3D Structure for #<Metabolite:0x00007fecad12db20>