MiMeDB: Showing metabocard for staphyloferrin A (MMDBc0056313)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:22:37 UTC

Update Date

2022-08-12 20:09:40 UTC

Metabolite ID

MMDBc0056313

Metabolite Identification

Common Name

staphyloferrin A

Description

3lhs belongs to the class of organic compounds known as pentacarboxylic acids and derivatives. These are carboxylic acids containing exactly five carboxyl groups. Based on a literature review very few articles have been published on 3lhs.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222222D          

 34 33  0  0  1  0            999 V2000
    1.6500    0.0000    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
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4125   -3.5724    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2375   -2.1434    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.2355    3.4914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5211    2.2539    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.0625   -3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -5.0013    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.1875    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -4.8099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164   -3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  8  2  1  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
 12  7  1  0  0  0  0
 13  8  1  0  0  0  0
 16  4  1  6  0  0  0
 16  6  1  0  0  0  0
 16 14  1  0  0  0  0
 17  5  1  1  0  0  0
 17  7  1  0  0  0  0
 17 15  1  0  0  0  0
 18  3  1  4  0  0  0
 18  9  2  0  0  0  0
  8 19  1  6  0  0  0
 19 10  2  0  0  0  0
 20  9  1  0  0  0  0
 10 21  1  4  0  0  0
 22 11  2  0  0  0  0
 23 11  1  0  0  0  0
 24 12  2  0  0  0  0
 25 12  1  0  0  0  0
 26 13  2  0  0  0  0
 27 13  1  0  0  0  0
 28 14  2  0  0  0  0
 29 14  1  0  0  0  0
 30 15  2  0  0  0  0
 31 15  1  0  0  0  0
 16 32  1  1  0  0  0
 17 33  1  6  0  0  0
  8 34  1  6  0  0  0
M  CHG  5  20  -1  21  -1  23  -1  25  -1  27  -1
M  END


  Mrv1652306172222222D          

 34 33  0  0  1  0            999 V2000
    1.6500    0.0000    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
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    2.6664    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4125   -3.5724    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2375   -2.1434    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.2355    3.4914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5211    2.2539    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.0625   -3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -5.0013    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.1875    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3020   -4.8099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164   -3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  8  2  1  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
 12  7  1  0  0  0  0
 13  8  1  0  0  0  0
 16  4  1  6  0  0  0
 16  6  1  0  0  0  0
 16 14  1  0  0  0  0
 17  5  1  1  0  0  0
 17  7  1  0  0  0  0
 17 15  1  0  0  0  0
 18  3  1  4  0  0  0
 18  9  2  0  0  0  0
  8 19  1  6  0  0  0
 19 10  2  0  0  0  0
 20  9  1  0  0  0  0
 10 21  1  4  0  0  0
 22 11  2  0  0  0  0
 23 11  1  0  0  0  0
 24 12  2  0  0  0  0
 25 12  1  0  0  0  0
 26 13  2  0  0  0  0
 27 13  1  0  0  0  0
 28 14  2  0  0  0  0
 29 14  1  0  0  0  0
 30 15  2  0  0  0  0
 31 15  1  0  0  0  0
 16 32  1  1  0  0  0
 17 33  1  6  0  0  0
  8 34  1  6  0  0  0
M  CHG  5  20  -1  21  -1  23  -1  25  -1  27  -1
M  END
> <DATABASE_ID>
MMDBc0056313

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](CCCN=C([O-])C[C@](O)(CC([O-])=O)C(O)=O)(N=C([O-])C[C@@](O)(CC([O-])=O)C(O)=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C17H24N2O14/c20-9(4-16(32,14(28)29)6-11(22)23)18-3-1-2-8(13(26)27)19-10(21)5-17(33,15(30)31)7-12(24)25/h8,32-33H,1-7H2,(H,18,20)(H,19,21)(H,22,23)(H,24,25)(H,26,27)(H,28,29)(H,30,31)/p-5/t8-,16+,17-/m1/s1

> <INCHI_KEY>
VJSIXUQLTJCRCS-DFQXCPINSA-I

> <FORMULA>
C17H19N2O14

> <MOLECULAR_WEIGHT>
475.342

> <EXACT_MASS>
475.086371199

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
40.184125721095604

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-{[(3R)-3,4-dicarboxy-3-hydroxy-1-oxidobutylidene]amino}-5-{[(3S)-3,4-dicarboxy-3-hydroxy-1-oxidobutylidene]amino}pentanoate

> <JCHEM_LOGP>
-3.9258844281961083

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
3.140155360832886

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.669074830155339

> <JCHEM_PKA_STRONGEST_BASIC>
6.116950945725085

> <JCHEM_POLAR_SURFACE_AREA>
306.29

> <JCHEM_REFRACTIVITY>
152.7118000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-{[(3R)-3,4-dicarboxy-3-hydroxy-1-oxidobutylidene]amino}-5-{[(3S)-3,4-dicarboxy-3-hydroxy-1-oxidobutylidene]amino}pentanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       3.080   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.620   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.700   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -5.335   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.240   4.207   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.540  -8.002   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.930   1.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.770  -4.001   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.906   4.977   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.080  -8.002   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.780   2.667   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.564  -7.438   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.240   2.667   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.770  -6.668   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       5.390   1.334   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0      -0.000  -2.667   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0       7.700   0.000   0.000  0.00  0.00           O-1
HETATM   21  O   UNK     0       2.310  -4.001   0.000  0.00  0.00           O-1
HETATM   22  O   UNK     0       7.906   6.517   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.573   4.207   0.000  0.00  0.00           O-1
HETATM   24  O   UNK     0       3.850  -6.668   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       3.850  -9.336   0.000  0.00  0.00           O-1
HETATM   26  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.770   1.334   0.000  0.00  0.00           O-1
HETATM   28  O   UNK     0      11.550   1.334   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      11.550   4.001   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -0.564  -8.978   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -1.897  -6.668   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       9.240   1.127   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       2.104  -5.898   0.000  0.00  0.00           O+0
HETATM   34  H   UNK     0       1.540  -0.000   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    8                                                       
CONECT    3    1   18                                                       
CONECT    4    9   16                                                       
CONECT    5   10   17                                                       
CONECT    6   11   16                                                       
CONECT    7   12   17                                                       
CONECT    8    2   13   19   34                                             
CONECT    9    4   18   20                                                  
CONECT   10    5   19   21                                                  
CONECT   11    6   22   23                                                  
CONECT   12    7   24   25                                                  
CONECT   13    8   26   27                                                  
CONECT   14   16   28   29                                                  
CONECT   15   17   30   31                                                  
CONECT   16    4    6   14   32                                             
CONECT   17    5    7   15   33                                             
CONECT   18    3    9                                                       
CONECT   19    8   10                                                       
CONECT   20    9                                                            
CONECT   21   10                                                            
CONECT   22   11                                                            
CONECT   23   11                                                            
CONECT   24   12                                                            
CONECT   25   12                                                            
CONECT   26   13                                                            
CONECT   27   13                                                            
CONECT   28   14                                                            
CONECT   29   14                                                            
CONECT   30   15                                                            
CONECT   31   15                                                            
CONECT   32   16                                                            
CONECT   33   17                                                            
CONECT   34    8                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   66    0
END

Synonyms

Not Available

Molecular Formula

C₁₇H₁₉N₂O₁₄

Average Mass

475.342

Monoisotopic Mass

475.086371199

IUPAC Name

(2R)-2-{[(3R)-3,4-dicarboxy-3-hydroxy-1-oxidobutylidene]amino}-5-{[(3S)-3,4-dicarboxy-3-hydroxy-1-oxidobutylidene]amino}pentanoate

Traditional Name

(2R)-2-{[(3R)-3,4-dicarboxy-3-hydroxy-1-oxidobutylidene]amino}-5-{[(3S)-3,4-dicarboxy-3-hydroxy-1-oxidobutylidene]amino}pentanoate

CAS Registry Number

Not Available

SMILES

[H][C@](CCCN=C([O-])C[C@](O)(CC([O-])=O)C(O)=O)(N=C([O-])C[C@@](O)(CC([O-])=O)C(O)=O)C([O-])=O

InChI Identifier

InChI=1S/C17H24N2O14/c20-9(4-16(32,14(28)29)6-11(22)23)18-3-1-2-8(13(26)27)19-10(21)5-17(33,15(30)31)7-12(24)25/h8,32-33H,1-7H2,(H,18,20)(H,19,21)(H,22,23)(H,24,25)(H,26,27)(H,28,29)(H,30,31)/p-5/t8-,16+,17-/m1/s1

InChI Key

VJSIXUQLTJCRCS-DFQXCPINSA-I

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentacarboxylic acids and derivatives. These are carboxylic acids containing exactly five carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Pentacarboxylic acids and derivatives

Direct Parent

Pentacarboxylic acids and derivatives

Alternative Parents

Substituents

Pentacarboxylic acid or derivatives
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid or derivatives
Fatty acyl
Fatty amide
N-acyl-amine
Tertiary alcohol
Carboxamide group
Carboxylic acid salt
Secondary carboxylic acid amide
Carboxylic acid
Alcohol
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.9	ChemAxon
pKa (Strongest Acidic)	2.67	ChemAxon
pKa (Strongest Basic)	6.12	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	306.29 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	152.71 m³·mol⁻¹	ChemAxon
Polarizability	40.18 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

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	Firmicutes	1	Human

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

72200157

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for staphyloferrin A (MMDBc0056313)

MOL for #<Metabolite:0x00007fecf0382888>

3D MOL for #<Metabolite:0x00007fecf0382888>

3D SDF for #<Metabolite:0x00007fecf0382888>

3D-SDF for #<Metabolite:0x00007fecf0382888>

PDB for #<Metabolite:0x00007fecf0382888>

3D PDB for #<Metabolite:0x00007fecf0382888>

SMILES for #<Metabolite:0x00007fecf0382888>

INCHI for #<Metabolite:0x00007fecf0382888>

Structure for #<Metabolite:0x00007fecf0382888>

3D Structure for #<Metabolite:0x00007fecf0382888>