MiMeDB: Showing metabocard for Staphyloferrin B (MMDBc0013317)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 04:38:48 UTC

Update Date

2022-08-31 06:35:55 UTC

Metabolite ID

MMDBc0013317

Metabolite Identification

Common Name

Staphyloferrin B

Description

staphyloferrin B belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. staphyloferrin B is a very strong basic compound (based on its pKa). A siderophore composed from L-2,3-diaminopropionic acid, citric acid, 1,2-diaminoethane and alpha-ketoglutaric acid units.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041411032D          

 32 31  0  0  1  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3349    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4783    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6052    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1927   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6052   -2.4454    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7638    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1927   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1927   -3.1599    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
   -5.9072    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1927    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.4302   -2.4454    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0493    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6052   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7638    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3677   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6052   -3.8743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3677   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6217    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9072    2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7802    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7802   -2.4454    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  8  7  1  0  0  0  0
  9  1  1  0  0  0  0
 10  2  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  8  1  0  0  0  0
 14  9  1  0  0  0  0
 16  5  1  0  0  0  0
 16  6  1  0  0  0  0
 16 15  1  6  0  0  0
  8 17  1  6  0  0  0
 18  3  1  4  0  0  0
 18 10  2  0  0  0  0
 19  4  1  4  0  0  0
 19 11  2  0  0  0  0
 20  7  1  4  0  0  0
 20 12  2  0  0  0  0
 21  9  2  0  0  0  0
 22 10  1  0  0  0  0
 23 11  1  0  0  0  0
 24 12  1  0  0  0  0
 25 13  2  0  0  0  0
 26 13  1  0  0  0  0
 27 14  1  0  0  0  0
 28 14  2  0  0  0  0
 29 15  2  0  0  0  0
 30 15  1  0  0  0  0
 16 31  1  1  0  0  0
  8 32  1  6  0  0  0
M  END


  Mrv0541 05041411032D          

 32 31  0  0  1  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3349    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4783    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6052    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1927   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6052   -2.4454    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7638    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1927   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1927   -3.1599    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
   -5.9072    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1927    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.4302   -2.4454    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0493    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6052   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7638    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3677   -0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6052   -3.8743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3677   -3.1599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6217    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9072    2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7802    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7802   -2.4454    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  8  7  1  0  0  0  0
  9  1  1  0  0  0  0
 10  2  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  8  1  0  0  0  0
 14  9  1  0  0  0  0
 16  5  1  0  0  0  0
 16  6  1  0  0  0  0
 16 15  1  6  0  0  0
  8 17  1  6  0  0  0
 18  3  1  4  0  0  0
 18 10  2  0  0  0  0
 19  4  1  4  0  0  0
 19 11  2  0  0  0  0
 20  7  1  4  0  0  0
 20 12  2  0  0  0  0
 21  9  2  0  0  0  0
 22 10  1  0  0  0  0
 23 11  1  0  0  0  0
 24 12  1  0  0  0  0
 25 13  2  0  0  0  0
 26 13  1  0  0  0  0
 27 14  1  0  0  0  0
 28 14  2  0  0  0  0
 29 15  2  0  0  0  0
 30 15  1  0  0  0  0
 16 31  1  1  0  0  0
  8 32  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0013317

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](N)(CN=C(O)C[C@@](O)(CC(O)=NCCN=C(O)CCC(=O)C(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H24N4O11/c17-8(13(25)26)7-20-12(24)6-16(31,15(29)30)5-11(23)19-4-3-18-10(22)2-1-9(21)14(27)28/h8,31H,1-7,17H2,(H,18,22)(H,19,23)(H,20,24)(H,25,26)(H,27,28)(H,29,30)/t8-,16-/m0/s1

> <INCHI_KEY>
SIAZVTIHOHTZDD-PWJLMRLQSA-N

> <FORMULA>
C16H24N4O11

> <MOLECULAR_WEIGHT>
448.382

> <EXACT_MASS>
448.14415763

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
41.508431874193946

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[(2-{[(3S)-3-({[(2S)-2-amino-2-carboxyethyl]-C-hydroxycarbonimidoyl}methyl)-3-carboxy-1,3-dihydroxypropylidene]amino}ethyl)-C-hydroxycarbonimidoyl]-2-oxobutanoic acid

> <ALOGPS_LOGP>
-2.37

> <JCHEM_LOGP>
-5.419077270362425

> <ALOGPS_LOGS>
-3.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.7446371996945307

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4930103627762028

> <JCHEM_PKA_STRONGEST_BASIC>
9.16143030910567

> <JCHEM_POLAR_SURFACE_AREA>
272.98999999999995

> <JCHEM_REFRACTIVITY>
98.0394

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.16e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-[(2-{[(3S)-3-({[(2S)-2-amino-2-carboxyethyl]-C-hydroxycarbonimidoyl}methyl)-3-carboxy-1,3-dihydroxypropylidene]amino}ethyl)-C-hydroxycarbonimidoyl]-2-oxobutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   32  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    9                                                       
CONECT    2    1   10                                                       
CONECT    3    4   18                                                       
CONECT    4    3   19                                                       
CONECT    5   11   16                                                       
CONECT    6   12   16                                                       
CONECT    7    8   20                                                       
CONECT    8    7   13   17   32                                             
CONECT    9    1   14   21                                                  
CONECT   10    2   18   22                                                  
CONECT   11    5   19   23                                                  
CONECT   12    6   20   24                                                  
CONECT   13    8   25   26                                                  
CONECT   14    9   27   28                                                  
CONECT   15   16   29   30                                                  
CONECT   16    5    6   15   31                                             
CONECT   17    8                                                            
CONECT   18    3   10                                                       
CONECT   19    4   11                                                       
CONECT   20    7   12                                                       
CONECT   21    9                                                            
CONECT   22   10                                                            
CONECT   23   11                                                            
CONECT   24   12                                                            
CONECT   25   13                                                            
CONECT   26   13                                                            
CONECT   27   14                                                            
CONECT   28   14                                                            
CONECT   29   15                                                            
CONECT   30   15                                                            
CONECT   31   16                                                            
CONECT   32    8                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   62    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₂₄N₄O₁₁

Average Mass

448.382

Monoisotopic Mass

448.14415763

IUPAC Name

4-[(2-{[(3S)-3-({[(2S)-2-amino-2-carboxyethyl]-C-hydroxycarbonimidoyl}methyl)-3-carboxy-1,3-dihydroxypropylidene]amino}ethyl)-C-hydroxycarbonimidoyl]-2-oxobutanoic acid

Traditional Name

4-[(2-{[(3S)-3-({[(2S)-2-amino-2-carboxyethyl]-C-hydroxycarbonimidoyl}methyl)-3-carboxy-1,3-dihydroxypropylidene]amino}ethyl)-C-hydroxycarbonimidoyl]-2-oxobutanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@](N)(CN=C(O)C[C@@](O)(CC(O)=NCCN=C(O)CCC(=O)C(O)=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C16H24N4O11/c17-8(13(25)26)7-20-12(24)6-16(31,15(29)30)5-11(23)19-4-3-18-10(22)2-1-9(21)14(27)28/h8,31H,1-7,17H2,(H,18,22)(H,19,23)(H,20,24)(H,25,26)(H,27,28)(H,29,30)/t8-,16-/m0/s1

InChI Key

SIAZVTIHOHTZDD-PWJLMRLQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Tricarboxylic acid or derivatives
Alpha-hydroxy acid
Alpha-keto acid
Fatty amide
Hydroxy acid
Keto acid
N-acyl-amine
Fatty acyl
Tertiary alcohol
Alpha-hydroxy ketone
Secondary carboxylic acid amide
Amino acid
Carboxamide group
Ketone
Carboxylic acid
Organic oxide
Primary aliphatic amine
Alcohol
Amine
Organonitrogen compound
Organooxygen compound
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Primary amine
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
Water Solubility	0.12 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-5.4	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	9.16	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	272.99 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	98.04 m³·mol⁻¹	ChemAxon
Polarizability	41.51 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	2	Human	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

CPD-12590

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46861568

PDB ID

Not Available

ChEBI ID

134612

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 B (MMDBc0013317)

MOL for #<Metabolite:0x00007fdb704773d8>

3D MOL for #<Metabolite:0x00007fdb704773d8>

3D SDF for #<Metabolite:0x00007fdb704773d8>

3D-SDF for #<Metabolite:0x00007fdb704773d8>

PDB for #<Metabolite:0x00007fdb704773d8>

3D PDB for #<Metabolite:0x00007fdb704773d8>

SMILES for #<Metabolite:0x00007fdb704773d8>

INCHI for #<Metabolite:0x00007fdb704773d8>

Structure for #<Metabolite:0x00007fdb704773d8>

3D Structure for #<Metabolite:0x00007fdb704773d8>