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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (87) Show 87 proteins XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-07 16:45:30 UTC

HMDB ID

HMDB0001491

Secondary Accession Numbers

HMDB01491

Metabolite Identification

Common Name

Pyridoxal 5'-phosphate

Description

Pyridoxal phosphate, also known as PLP, pyridoxal 5'-phosphate or P5P, is the active form of vitamin B6. It is a coenzyme in a variety of enzymatic reactions. Pyridoxal 5'-phosphate belongs to the class of organic compounds known as pyridoxals and derivatives. Pyridoxals and derivatives are compounds containing a pyridoxal moiety, which consists of a pyridine ring substituted at positions 2,3,4, and 5 by a methyl group, a hydroxyl group, a carbaldehyde group, and a hydroxymethyl group, respectively. Pyridoxal 5'-phosphate is a drug which is used for nutritional supplementation and for treating dietary shortage or imbalance. Pyridoxal 5'-phosphate exists in all living species, ranging from bacteria to humans. In humans, pyridoxal 5'-phosphate is involved in glycine and serine metabolism. Outside of the human body, pyridoxal 5'-phosphate is found, on average, in the highest concentration within cow milk. Pyridoxal 5'-phosphate has also been detected, but not quantified in several different foods, such as soursops, italian sweet red peppers, muscadine grapes, european plums, and blackcurrants. Pyridoxal 5'-phosphate, with regard to humans, has been found to be associated with several diseases such as epilepsy, early-onset, vitamin B6-dependent, odontohypophosphatasia, pyridoxamine 5-prime-phosphate oxidase deficiency, and hypophosphatasia. Pyridoxal 5'-phosphate has also been linked to the inborn metabolic disorder celiac disease.

Structure

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

114
  Mrv1652309042000232D          

 16 16  0  0  0  0            999 V2000
    6.3799    0.2063    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.6655   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930    0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7925   -0.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0944    0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9674    0.9207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -1.4438    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  2  0  0  0  0
  2 11  1  0  0  0  0
  3 12  1  0  0  0  0
  6 16  2  0  0  0  0
  8 13  2  0  0  0  0
  8 14  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 14  2  0  0  0  0
 10 12  2  0  0  0  0
 10 16  1  0  0  0  0
 12 13  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001491

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=NC=C(COP(O)(O)=O)C(C=O)=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)

> <INCHI_KEY>
NGVDGCNFYWLIFO-UHFFFAOYSA-N

> <FORMULA>
C8H10NO6P

> <MOLECULAR_WEIGHT>
247.1419

> <EXACT_MASS>
247.024573569

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
20.898887181263255

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(4-formyl-5-hydroxy-6-methylpyridin-3-yl)methoxy]phosphonic acid

> <ALOGPS_LOGP>
-0.55

> <JCHEM_LOGP>
-2.0856087036128135

> <ALOGPS_LOGS>
-1.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.691277029499376

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.680298610655746

> <JCHEM_PKA_STRONGEST_BASIC>
4.109012435085948

> <JCHEM_POLAR_SURFACE_AREA>
116.95

> <JCHEM_REFRACTIVITY>
54.746300000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.70e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridoxal phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 114                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  P   UNK     0      11.909   0.385   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      10.576  -0.385   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       3.907   0.385   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      12.679  -0.949   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      13.243   1.155   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       5.241   2.695   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      11.139   1.719   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       6.574  -2.695   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       7.908  -0.385   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.574   0.385   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.242   0.385   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.241  -0.385   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.241  -1.925   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.908  -1.925   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.907  -2.695   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.574   1.925   0.000  0.00  0.00           C+0
CONECT    1    2    4    5    7                                             
CONECT    2    1   11                                                       
CONECT    3   12                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6   16                                                            
CONECT    7    1                                                            
CONECT    8   13   14                                                       
CONECT    9   10   11   14                                                  
CONECT   10    9   12   16                                                  
CONECT   11    2    9                                                       
CONECT   12    3   10   13                                                  
CONECT   13    8   12   15                                                  
CONECT   14    8    9                                                       
CONECT   15   13                                                            
CONECT   16    6   10                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

COMPND    HMDB0001491
HETATM    1  C1  UNL     1      -3.905  -1.496  -0.335  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.504  -0.954  -0.225  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.485  -1.803  -0.095  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.231  -1.333   0.004  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.077   0.014  -0.021  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.486   0.494   0.092  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.302  -0.608   0.214  1.00  0.00           O  
HETATM    8  P1  UNL     1       3.924  -0.235   0.351  1.00  0.00           P  
HETATM    9  O2  UNL     1       4.217   0.086   1.809  1.00  0.00           O  
HETATM   10  O3  UNL     1       4.824  -1.605  -0.104  1.00  0.00           O  
HETATM   11  O4  UNL     1       4.386   1.060  -0.624  1.00  0.00           O  
HETATM   12  C6  UNL     1      -0.983   0.887  -0.156  1.00  0.00           C  
HETATM   13  C7  UNL     1      -0.719   2.303  -0.188  1.00  0.00           C  
HETATM   14  O5  UNL     1      -1.699   3.114  -0.313  1.00  0.00           O  
HETATM   15  C8  UNL     1      -2.258   0.392  -0.256  1.00  0.00           C  
HETATM   16  O6  UNL     1      -3.339   1.275  -0.393  1.00  0.00           O  
HETATM   17  H1  UNL     1      -4.200  -1.427  -1.410  1.00  0.00           H  
HETATM   18  H2  UNL     1      -3.897  -2.572  -0.072  1.00  0.00           H  
HETATM   19  H3  UNL     1      -4.593  -0.928   0.328  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.623  -2.006   0.112  1.00  0.00           H  
HETATM   21  H5  UNL     1       1.762   1.147  -0.760  1.00  0.00           H  
HETATM   22  H6  UNL     1       1.528   1.117   1.020  1.00  0.00           H  
HETATM   23  H7  UNL     1       4.274  -2.424   0.018  1.00  0.00           H  
HETATM   24  H8  UNL     1       4.437   1.870  -0.046  1.00  0.00           H  
HETATM   25  H9  UNL     1       0.259   2.708  -0.113  1.00  0.00           H  
HETATM   26  H10 UNL     1      -4.285   0.924  -0.468  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3    3   15
CONECT    3    4
CONECT    4    5    5   20
CONECT    5    6   12
CONECT    6    7   21   22
CONECT    7    8
CONECT    8    9    9   10   11
CONECT   10   23
CONECT   11   24
CONECT   12   13   15   15
CONECT   13   14   14   25
CONECT   15   16
CONECT   16   26
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3-Hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinecarboxaldehyde	ChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphate	ChEBI
Codecarboxylase	ChEBI
Phosphoric acid mono-(4-formyl-5-hydroxy-6-methyl-pyridin-3-ylmethyl) ester	ChEBI
PLP	ChEBI
Pyridoxal 5'-(dihydrogen phosphate)	ChEBI
Pyridoxal 5-monophosphoric acid ester	ChEBI
Pyridoxal 5-phosphate	ChEBI
Pyridoxal phosphate	ChEBI
PYRIDOXAL-5'-phosphATE	ChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphoric acid	Generator
Phosphate mono-(4-formyl-5-hydroxy-6-methyl-pyridin-3-ylmethyl) ester	Generator
Pyridoxal 5'-(dihydrogen phosphoric acid)	Generator
Pyridoxal 5-monophosphate ester	Generator
Pyridoxal 5-phosphoric acid	Generator
Pyridoxal phosphoric acid	Generator
PYRIDOXAL-5'-phosphoric acid	Generator
Pyridoxal 5'-phosphoric acid	Generator
Apolon b6	HMDB
Biosechs	HMDB
Coenzyme b6	HMDB
Hairoxal	HMDB
Hexermin-p	HMDB
Hi-pyridoxin	HMDB
Hiadelon	HMDB
Himitan	HMDB
PAL-p	HMDB
Phosphopyridoxal	HMDB
Phosphopyridoxal coenzyme	HMDB
Pidopidon	HMDB
Piodel	HMDB
Pydoxal	HMDB
Pyridoxal p	HMDB
Pyridoxal-p	HMDB
Pyridoxyl phosphate	HMDB
Pyromijin	HMDB
Sechvitan	HMDB
Vitahexin-p	HMDB
Vitazechs	HMDB
Phosphate, pyridoxal	HMDB
Pyridoxal 5 phosphate	HMDB

Chemical Formula

C₈H₁₀NO₆P

Average Molecular Weight

247.1419

Monoisotopic Molecular Weight

247.024573569

IUPAC Name

[(4-formyl-5-hydroxy-6-methylpyridin-3-yl)methoxy]phosphonic acid

Traditional Name

pyridoxal phosphate

CAS Registry Number

54-47-7

SMILES

CC1=NC=C(COP(O)(O)=O)C(C=O)=C1O

InChI Identifier

InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)

InChI Key

NGVDGCNFYWLIFO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridoxals and derivatives. Pyridoxals and derivatives are compounds containing a pyridoxal moiety, which consists of a pyridine ring substituted at positions 2,3,4, and 5 by a methyl group, a hydroxyl group, a carbaldehyde group, and a hydroxymethyl group, respectively.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridine carboxaldehydes

Direct Parent

Pyridoxals and derivatives

Alternative Parents

Substituents

Pyridoxal
Aryl-aldehyde
Monoalkyl phosphate
Hydroxypyridine
Methylpyridine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Vinylogous acid
Heteroaromatic compound
Azacycle
Organopnictogen compound
Aldehyde
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

monohydroxypyridine (CHEBI:18405 )
pyridinecarbaldehyde (CHEBI:18405 )
methylpyridines (CHEBI:18405 )
vitamin B6 phosphate (CHEBI:18405 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Organelle

Mitochondria

Mitochondria (HMDB: HMDB0001491)

Mitochondria (HMDB: HMDB0001491)
Membrane (HMDB: HMDB0001491)

Biofluid or Excreta

Blood (HMDB: HMDB0001491)
Cerebrospinal fluid (HMDB: HMDB0001491)

Tissue substructure

Muscle (HMDB: HMDB0001491)

Cell

Organ

Kidney (HMDB: HMDB0001491)
Liver (HMDB: HMDB0001491)

Tissue

Muscle tissue

Skeletal Muscle (HMDB: HMDB0001491)

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 16277678)
Cerebrospinal Fluid (CSF) (PMID: 6182788)

Excreta

Biofluid or Excreta

Urine (PMID: 32966057)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0001491)

Source

Endogenous

Endogenous (HMDB: HMDB0001491)

Plant

Animal

Animal (HMDB: HMDB0001491)

Exogenous

Food

Food (HMDB: HMDB0001491)

Animal origin

Poultry

Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)
Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)

Equine

Horse (FooDB: FOOD00378)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Herb and spice mixture

Curry powder (FooDB: FOOD00678)

Herbs and Spices (FooDB: FOOD00866)

Vegetable

Cabbage

Onion-family vegetable

Allium (FooDB: FOOD00005)
Garden onion (FooDB: FOOD00006)
Leek (FooDB: FOOD00007)
Garden onion (var.) (FooDB: FOOD00226)
Shallot (FooDB: FOOD00243)
Wild leek (FooDB: FOOD00396)
Red onion (FooDB: FOOD00962)
Green onion (FooDB: FOOD00963)
Onion-family vegetables (FooDB: FOOD00855)

Root vegetable

Shoot vegetable

Leaf vegetable

Common beet (FooDB: FOOD00025)
Endive (FooDB: FOOD00048)
Rocket salad (ssp.) (FooDB: FOOD00077)
Swamp cabbage (FooDB: FOOD00091)
Lettuce (FooDB: FOOD00095)
Garden cress (FooDB: FOOD00099)
Spinach (FooDB: FOOD00178)
Swiss chard (FooDB: FOOD00237)
Chicory leaves (FooDB: FOOD00250)
Garland chrysanthemum (FooDB: FOOD00333)
Corn salad (FooDB: FOOD00340)
Jute (FooDB: FOOD00389)
Lambsquarters (FooDB: FOOD00394)
Malabar spinach (FooDB: FOOD00404)
New Zealand spinach (FooDB: FOOD00415)
Yautia (FooDB: FOOD00510)
Ostrich fern (FooDB: FOOD00556)
Romaine lettuce (FooDB: FOOD00888)
Iceberg lettuce (FooDB: FOOD00973)
Pea shoots (FooDB: FOOD00975)
Yau choy (FooDB: FOOD00976)
Water spinach (FooDB: FOOD00977)
Rocket salad (FooDB: FOOD00244)
Green vegetables (FooDB: FOOD00872)

Fruit vegetable

Pepper (FooDB: FOOD00040)
Olive (FooDB: FOOD00121)
Avocado (FooDB: FOOD00130)
Garden tomato (FooDB: FOOD00171)
Cherry tomato (FooDB: FOOD00172)
Garden tomato (var.) (FooDB: FOOD00173)
Eggplant (FooDB: FOOD00174)
Pepper (C. baccatum) (FooDB: FOOD00231)
Pepper (C. chinense) (FooDB: FOOD00232)
Pepper (Capsicum) (FooDB: FOOD00233)
Groundcherry (FooDB: FOOD00371)
Pepper (C. frutescens) (FooDB: FOOD00428)
Mexican groundcherry (FooDB: FOOD00491)
Pepper (C. pubescens) (FooDB: FOOD00849)
Green bell pepper (FooDB: FOOD00877)
Yellow bell pepper (FooDB: FOOD00878)
Orange bell pepper (FooDB: FOOD00879)
Red bell pepper (FooDB: FOOD00880)
Italian sweet red pepper (FooDB: FOOD00881)
Jalapeno pepper (FooDB: FOOD00955)
Cubanelle pepper (FooDB: FOOD00971)

Tuber

Stalk vegetable

Other vegetable

Giant butterbur (FooDB: FOOD00314)
Carob (FooDB: FOOD00321)
Chinese water chestnut (FooDB: FOOD00332)
Horseradish tree (FooDB: FOOD00379)
Sacred lotus (FooDB: FOOD00402)
Nopal (FooDB: FOOD00416)
Okra (FooDB: FOOD00420)
Sesbania flower (FooDB: FOOD00469)
Agave (FooDB: FOOD00563)
Narrowleaf cattail (FooDB: FOOD00564)
Heart of palm (FooDB: FOOD00718)
Tree fern (FooDB: FOOD00797)

Mushroom

Castanospermum australe (FooDB: FOOD00893)
Gentiana lutea (FooDB: FOOD00894)
Juniperus communis (FooDB: FOOD00895)
Albizia gummifera (FooDB: FOOD00896)

Brassica

Brassicas (FooDB: FOOD00857)

Fruit

Tropical fruit

Citrus

Lime (FooDB: FOOD00053)
Lemon (FooDB: FOOD00054)
Pummelo (FooDB: FOOD00055)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Sweet orange (FooDB: FOOD00057)
Grapefruit/Pummelo hybrid (FooDB: FOOD00255)
Grapefruit (FooDB: FOOD00256)
Persian lime (FooDB: FOOD00543)
Sour orange (FooDB: FOOD00918)
Mikan (FooDB: FOOD00932)
Clementine (FooDB: FOOD00959)
Citrus (FooDB: FOOD00859)

Pome

Berry

Black crowberry (FooDB: FOOD00075)
Strawberry (FooDB: FOOD00083)
Black huckleberry (FooDB: FOOD00084)
Sea-buckthornberry (FooDB: FOOD00087)
Mulberry (FooDB: FOOD00116)
Black mulberry (FooDB: FOOD00117)
Black chokeberry (FooDB: FOOD00136)
Blackcurrant (FooDB: FOOD00155)
Redcurrant (FooDB: FOOD00156)
Gooseberry (FooDB: FOOD00157)
Cloudberry (FooDB: FOOD00161)
Red raspberry (FooDB: FOOD00162)
Black raspberry (FooDB: FOOD00163)
Black elderberry (FooDB: FOOD00166)
Rowanberry (FooDB: FOOD00176)
Vaccinium (Blueberry, Cranberry, Huckleberry) (FooDB: FOOD00188)
Lowbush blueberry (FooDB: FOOD00189)
Sparkleberry (FooDB: FOOD00190)
Highbush blueberry (FooDB: FOOD00191)
American cranberry (FooDB: FOOD00192)
Bilberry (FooDB: FOOD00193)
Lingonberry (FooDB: FOOD00194)
Muscadine grape (FooDB: FOOD00203)
Common grape (FooDB: FOOD00204)
Arctic blackberry (FooDB: FOOD00207)
Bayberry (FooDB: FOOD00209)
Elliott's blueberry (FooDB: FOOD00210)
Canada blueberry (FooDB: FOOD00211)
Bog bilberry (FooDB: FOOD00212)
Buffalo currant (FooDB: FOOD00213)
European cranberry (FooDB: FOOD00217)
Deerberry (FooDB: FOOD00218)
Cascade huckleberry (FooDB: FOOD00220)
Oval-leaf huckleberry (FooDB: FOOD00221)
Evergreen huckleberry (FooDB: FOOD00222)
Red huckleberry (FooDB: FOOD00223)
Summer grape (FooDB: FOOD00227)
Fox grape (FooDB: FOOD00228)
Half-highbush blueberry (FooDB: FOOD00248)
Jostaberry (FooDB: FOOD00257)
Sweet rowanberry (FooDB: FOOD00265)
Skunk currant (FooDB: FOOD00267)
Squashberry (FooDB: FOOD00344)
Elderberry (FooDB: FOOD00358)
Grape (FooDB: FOOD00369)
Alaska blueberry (FooDB: FOOD00380)
Loganberry (FooDB: FOOD00400)
Ohelo berry (FooDB: FOOD00419)
Salmonberry (FooDB: FOOD00456)
Strawberry guava (FooDB: FOOD00482)
Boysenberry (FooDB: FOOD00542)
Chinese bayberry (FooDB: FOOD00852)
Saskatoon berry (FooDB: FOOD00884)
Nanking cherry (FooDB: FOOD00885)
Rabbiteye blueberry (FooDB: FOOD00898)
Blackberry (FooDB: FOOD00906)
Partridge berry (FooDB: FOOD00931)
Green grape (FooDB: FOOD00964)
Red grape (FooDB: FOOD00965)
Black plum (FooDB: FOOD00966)
Black raisin (FooDB: FOOD00968)
Chinese plum (FooDB: FOOD00978)
Green plum (FooDB: FOOD00979)
Wampee (FooDB: FOOD00980)
Goji (FooDB: FOOD00982)
Monk fruit (FooDB: FOOD00983)
Hawthorn (FooDB: FOOD00985)
Lantern fruit (FooDB: FOOD00986)
Cape gooseberry (FooDB: FOOD00988)
Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)

Other fruit

Fig (FooDB: FOOD00081)
Date (FooDB: FOOD00135)
Jujube (FooDB: FOOD00388)

Drupe

Prunus (Cherry, Plum) (FooDB: FOOD00143)
Apricot (FooDB: FOOD00144)
Sweet cherry (FooDB: FOOD00145)
Sour cherry (FooDB: FOOD00146)
European plum (FooDB: FOOD00147)
Peach (FooDB: FOOD00149)
Nectarine (FooDB: FOOD00229)
Peach (var.) (FooDB: FOOD00230)
Common chokecherry (FooDB: FOOD00562)

Fruits (FooDB: FOOD00871)

Nut

Cashew nut (FooDB: FOOD00011)
Peanut (FooDB: FOOD00016)
Brazil nut (FooDB: FOOD00024)
Pecan nut (FooDB: FOOD00044)
Chestnut (FooDB: FOOD00045)
Common hazelnut (FooDB: FOOD00062)
Black walnut (FooDB: FOOD00093)
Common walnut (FooDB: FOOD00094)
Pine nut (FooDB: FOOD00138)
Pistachio (FooDB: FOOD00140)
Almond (FooDB: FOOD00148)
Macadamia nut (M. tetraphylla) (FooDB: FOOD00225)
Japanese walnut (FooDB: FOOD00240)
Acorn (FooDB: FOOD00282)
Beech nut (FooDB: FOOD00299)
Butternut (FooDB: FOOD00316)
Chinese chestnut (FooDB: FOOD00331)
European chestnut (FooDB: FOOD00363)
Hazelnut (FooDB: FOOD00376)
Hickory nut (FooDB: FOOD00377)
Japanese chestnut (FooDB: FOOD00385)
Pili nut (FooDB: FOOD00432)
Colorado pinyon (FooDB: FOOD00433)
Macadamia nut (FooDB: FOOD00525)
Walnut (FooDB: FOOD00608)
Mixed nuts (FooDB: FOOD00771)
Nuts (FooDB: FOOD00869)

Cereal and cereal product

Cereal

Cereal product

Dough

Sourdough (FooDB: FOOD00275)

Leavened bread

Flat bread

Other bread

Potato bread (FooDB: FOOD00811)
Other bread (FooDB: FOOD00269)

Sweet bread

Raisin bread (FooDB: FOOD00817)

Cereals and cereal products (FooDB: FOOD00858)

Pulse

Pea

Lentil

Lentils (FooDB: FOOD00098)

Other pulse

Lupine (FooDB: FOOD00104)
White lupine (FooDB: FOOD00403)

Bean

Green lentil (FooDB: FOOD00970)
Pulses (FooDB: FOOD00867)

Gourd

Watermelon (FooDB: FOOD00052)
Muskmelon (FooDB: FOOD00064)
Cucumber (FooDB: FOOD00065)
Cucurbita (FooDB: FOOD00066)
Bitter gourd (FooDB: FOOD00115)
Winter squash (FooDB: FOOD00283)
Butternut squash (FooDB: FOOD00317)
Calabash (FooDB: FOOD00318)
Chayote (FooDB: FOOD00325)
Towel gourd (FooDB: FOOD00492)
Wax gourd (FooDB: FOOD00499)
Tinda (FooDB: FOOD00559)
Horned melon (FooDB: FOOD00761)
Sunburst squash (pattypan squash) (FooDB: FOOD00874)
Green zucchini (FooDB: FOOD00875)
Yellow zucchini (FooDB: FOOD00876)
Japanese pumpkin (FooDB: FOOD00886)
Acorn squash (FooDB: FOOD00972)
Cantaloupe melon (FooDB: FOOD00984)

Coffee and coffee product

Coffee

Arabica coffee (FooDB: FOOD00059)
Robusta coffee (FooDB: FOOD00060)

Soy

Soy bean (FooDB: FOOD00085)

Soy product

Dish

Other dish

Taco shell (FooDB: FOOD00991)
Tostada shell (FooDB: FOOD00992)

Tea

Herbal tea

Hibiscus tea (FooDB: FOOD00723)
Greenthread tea (FooDB: FOOD00820)

Baking good

Wrapper

Wonton wrapper (FooDB: FOOD00818)

Abalone (FooDB: FOOD00279)
Conch (FooDB: FOOD00611)

Milk and milk product

Unfermented milk

Milk (Cow) (FooDB: FOOD00618)

Cocoa and cocoa product

Cocoa

Cocoa bean (FooDB: FOOD00182)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Malate-Aspartate Shuttle (HMDB: HMDB0001491)
Glucose-Alanine Cycle (HMDB: HMDB0001491)
Vitamin B6 Metabolism (HMDB: HMDB0001491)
Alanine Metabolism (PathBank: SMP0000055)
Aspartate Metabolism (PathBank: SMP0000067)
Glutamate Metabolism (PathBank: SMP0000072)
Taurine and Hypotaurine Metabolism (PathBank: SMP0000021)
Selenoamino Acid Metabolism (PathBank: SMP0000029)
Ammonia Recycling (PathBank: SMP0000009)
Arginine and Proline Metabolism (PathBank: SMP0000020)
beta-Alanine Metabolism (PathBank: SMP0000007)
Carnitine Synthesis (PathBank: SMP0000465)
Catecholamine Biosynthesis (PathBank: SMP0000012)
Cysteine Metabolism (PathBank: SMP0000013)
Folate Metabolism (PathBank: SMP0000053)
Homocysteine Degradation (PathBank: SMP0000455)
Lysine Degradation (PathBank: SMP0000037)
Spermidine and Spermine Biosynthesis (PathBank: SMP0000445)
Phenylalanine and Tyrosine Metabolism (PathBank: SMP0000008)
Histidine Metabolism (PathBank: SMP0000044)
Valine, Leucine, and Isoleucine Degradation (PathBank: SMP0000032)
Methionine Metabolism (PathBank: SMP0000033)
Tyrosine Metabolism (PathBank: SMP0000006)
Sphingolipid Metabolism (PathBank: SMP0000034)
Propanoate Metabolism (PathBank: SMP0000016)
Starch and Sucrose Metabolism (PathBank: SMP0000058)
Glycine and Serine Metabolism (PathBank: SMP0000004)
Porphyrin Metabolism (PathBank: SMP0000024)
Urea Cycle (PathBank: SMP0000059)
Tryptophan Metabolism (PathBank: SMP0000063)
Threonine and 2-Oxobutanoate Degradation (PathBank: SMP0000452)
Cysteine Biosynthesis (PathBank: SMP0000821)
Threonine Biosynthesis (PathBank: SMP0000837)
Phenylalanine Metabolism (PathBank: SMP0000938)
Sulfur Metabolism (PathBank: SMP0000939)
Sulfur Metabolism (Butanesulfonate) (PathBank: SMP0000940)
Sulfur Metabolism (Propanesulfonate) (PathBank: SMP0000941)
Sulfur Metabolism (Ethanesulfonate) (PathBank: SMP0000942)
Sulfur Metabolism (Isethionate) (PathBank: SMP0000943)
Sulfur Metabolism (Methanesulfonate) (PathBank: SMP0000944)
Secondary Metabolites: Enterobacterial Common Antigen Biosynthesis (PathBank: SMP0000975)
Secondary Metabolites: Trehalose Biosynthesis and Metabolism (PathBank: SMP0000984)
Secondary Metabolites: Enterobacterial Common Antigen Biosynthesis 2 (PathBank: SMP0002059)
Secondary Metabolites: Enterobacterial Common Antigen Biosynthesis 3 (PathBank: SMP0002060)
Porphyrin Metabolism (PathBank: SMP0002363)
Sphingolipid Metabolism (PathBank: SMP0002378)
Starch and Sucrose Metabolism (PathBank: SMP0002380)
Vitamin B6 (PathBank: SMP0002387)
Choline Biosynthesis I (PathBank: SMP0012026)
Choline Biosynthesis II (PathBank: SMP0012027)
Plastoquinol-9 Biosynthesis (PathBank: SMP0012043)
Thio-Molybdenum Cofactor Biosynthesis (PathBank: SMP0012046)
Glycine Betaine Biosynthesis I (PathBank: SMP0012047)
Glycine Betaine Biosynthesis II (PathBank: SMP0012048)
Butanoate Metabolism (PathBank: SMP0012467)
Phosphatidylcholine Biosynthesis (PathBank: SMP0014205)
Phosphatidylethanolamine Biosynthesis (PathBank: SMP0014208)
Isoquinoline Alkaloid Biosynthesis (PathBank: SMP0063471)
Vitamin B6 Metabolism (PathBank: SMP0063472)
Tropane, Piperidine, and Pyridine Alkaloid Biosynthesis (PathBank: SMP0063474)
Phosphatidylethanolamine Biosynthesis PE(16:0/16:0) (PathBank: SMP0071720)
Phosphatidylethanolamine Biosynthesis PE(16:0/18:0) (PathBank: SMP0071721)
Phosphatidylethanolamine Biosynthesis PE(16:0/18:1(9Z)) (PathBank: SMP0071722)
Phosphatidylethanolamine Biosynthesis PE(16:0/18:1(11Z)) (PathBank: SMP0071723)
Phosphatidylethanolamine Biosynthesis PE(16:0/18:2(9Z,12Z)) (PathBank: SMP0071724)
Phosphatidylethanolamine Biosynthesis PE(16:0/18:3(6Z,9Z,12Z)) (PathBank: SMP0071725)
Phosphatidylethanolamine Biosynthesis PE(16:0/18:3(9Z,12Z,15Z)) (PathBank: SMP0071726)
Phosphatidylethanolamine Biosynthesis PE(16:0/20:0) (PathBank: SMP0071727)
Phosphatidylethanolamine Biosynthesis PE(16:0/20:1(11Z)) (PathBank: SMP0071728)
Phosphatidylethanolamine Biosynthesis PE(16:0/20:1(13Z)) (PathBank: SMP0071729)
Phosphatidylethanolamine Biosynthesis PE(16:0/22:0) (PathBank: SMP0071730)
Phosphatidylethanolamine Biosynthesis PE(16:0/22:1(13Z)) (PathBank: SMP0071731)
Phosphatidylethanolamine Biosynthesis PE(18:0/18:0) (PathBank: SMP0071732)
Phosphatidylethanolamine Biosynthesis PE(18:0/18:1(9Z)) (PathBank: SMP0071733)
Phosphatidylethanolamine Biosynthesis PE(18:0/18:1(11Z)) (PathBank: SMP0071734)
Phosphatidylethanolamine Biosynthesis PE(18:0/18:2(9Z,12Z)) (PathBank: SMP0071735)
Phosphatidylethanolamine Biosynthesis PE(18:0/18:3(6Z,9Z,12Z)) (PathBank: SMP0071736)
Phosphatidylethanolamine Biosynthesis PE(18:0/18:3(9Z,12Z,15Z)) (PathBank: SMP0071737)
Phosphatidylethanolamine Biosynthesis PE(18:0/20:0) (PathBank: SMP0071738)
Phosphatidylethanolamine Biosynthesis PE(18:0/20:1(11Z)) (PathBank: SMP0071739)
Phosphatidylethanolamine Biosynthesis PE(18:0/20:1(13Z)) (PathBank: SMP0071740)
Phosphatidylethanolamine Biosynthesis PE(18:0/22:0) (PathBank: SMP0071741)
Phosphatidylethanolamine Biosynthesis PE(18:0/22:1(13Z)) (PathBank: SMP0071742)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/18:1(9Z)) (PathBank: SMP0071743)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/18:1(11Z)) (PathBank: SMP0071744)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/18:2(9Z,12Z)) (PathBank: SMP0071745)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/18:3(6Z,9Z,12Z)) (PathBank: SMP0071746)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/18:3(9Z,12Z,15Z)) (PathBank: SMP0071747)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/20:0) (PathBank: SMP0071748)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/20:1(11Z)) (PathBank: SMP0071749)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/20:1(13Z)) (PathBank: SMP0071750)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/22:0) (PathBank: SMP0071751)
Phosphatidylethanolamine Biosynthesis PE(18:1(9Z)/22:1(13Z)) (PathBank: SMP0071752)
Phosphatidylethanolamine Biosynthesis PE(18:1(11Z)/18:1(11Z)) (PathBank: SMP0071753)
Phosphatidylethanolamine Biosynthesis PE(18:1(11Z)/18:2(9Z,12Z)) (PathBank: SMP0071754)
Phosphatidylethanolamine Biosynthesis PE(18:1(11Z)/18:3(6Z,9Z,12Z)) (PathBank: SMP0071755)
Phosphatidylethanolamine Biosynthesis PE(18:1(11Z)/18:3(9Z,12Z,15Z)) (PathBank: SMP0071756)
Phosphatidylethanolamine Biosynthesis PE(18:1(11Z)/20:0) (PathBank: SMP0071757)
Phosphatidylethanolamine Biosynthesis PE(18:1(11Z)/20:1(11Z)) (PathBank: SMP0071758)
Phosphatidylethanolamine Biosynthesis PE(18:1(11Z)/20:1(13Z)) (PathBank: SMP0071759)
Phosphatidylethanolamine Biosynthesis PE(18:1(11Z)/22:0) (PathBank: SMP0071760)
Phosphatidylethanolamine Biosynthesis PE(18:1(11Z)/22:1(13Z)) (PathBank: SMP0071761)
Phosphatidylethanolamine Biosynthesis PE(18:2(9Z,12Z)/18:2(9Z,12Z)) (PathBank: SMP0071762)
Phosphatidylethanolamine Biosynthesis PE(18:2(9Z,12Z)/18:3(6Z,9Z,12Z)) (PathBank: SMP0071763)
Phosphatidylethanolamine Biosynthesis PE(18:2(9Z,12Z)/18:3(9Z,12Z,15Z)) (PathBank: SMP0071764)
Phosphatidylethanolamine Biosynthesis PE(18:2(9Z,12Z)/20:0) (PathBank: SMP0071765)
Phosphatidylethanolamine Biosynthesis PE(18:2(9Z,12Z)/20:1(11Z)) (PathBank: SMP0071766)
Phosphatidylethanolamine Biosynthesis PE(18:2(9Z,12Z)/20:1(13Z)) (PathBank: SMP0071767)
Phosphatidylethanolamine Biosynthesis PE(18:2(9Z,12Z)/22:0) (PathBank: SMP0071768)
Phosphatidylethanolamine Biosynthesis PE(18:2(9Z,12Z)/22:1(13Z)) (PathBank: SMP0071769)
Phosphatidylethanolamine Biosynthesis PE(18:3(6Z,9Z,12Z)/18:3(6Z,9Z,12Z)) (PathBank: SMP0071770)
Phosphatidylethanolamine Biosynthesis PE(18:3(6Z,9Z,12Z)/18:3(9Z,12Z,15Z)) (PathBank: SMP0071771)
Phosphatidylethanolamine Biosynthesis PE(18:3(6Z,9Z,12Z)/20:0) (PathBank: SMP0071772)
Phosphatidylethanolamine Biosynthesis PE(18:3(6Z,9Z,12Z)/20:1(11Z)) (PathBank: SMP0071773)
Phosphatidylethanolamine Biosynthesis PE(18:3(6Z,9Z,12Z)/20:1(13Z)) (PathBank: SMP0071774)
Phosphatidylethanolamine Biosynthesis PE(18:3(6Z,9Z,12Z)/22:0) (PathBank: SMP0071775)
Phosphatidylethanolamine Biosynthesis PE(18:3(6Z,9Z,12Z)/22:1(13Z)) (PathBank: SMP0071776)
Phosphatidylethanolamine Biosynthesis PE(18:3(9Z,12Z,15Z)/18:3(9Z,12Z,15Z)) (PathBank: SMP0071777)
Phosphatidylethanolamine Biosynthesis PE(18:3(9Z,12Z,15Z)/20:0) (PathBank: SMP0071778)
Phosphatidylethanolamine Biosynthesis PE(18:3(9Z,12Z,15Z)/20:1(11Z)) (PathBank: SMP0071779)
Phosphatidylethanolamine Biosynthesis PE(18:3(9Z,12Z,15Z)/20:1(13Z)) (PathBank: SMP0071780)
Phosphatidylethanolamine Biosynthesis PE(18:3(9Z,12Z,15Z)/22:0) (PathBank: SMP0071781)
Phosphatidylethanolamine Biosynthesis PE(18:3(9Z,12Z,15Z)/22:1(13Z)) (PathBank: SMP0071782)
Phosphatidylethanolamine Biosynthesis PE(20:0/20:0) (PathBank: SMP0071783)
Phosphatidylethanolamine Biosynthesis PE(20:0/20:1(11Z)) (PathBank: SMP0071784)
Phosphatidylethanolamine Biosynthesis PE(20:0/20:1(13Z)) (PathBank: SMP0071785)
Phosphatidylethanolamine Biosynthesis PE(20:0/22:0) (PathBank: SMP0071786)
Phosphatidylethanolamine Biosynthesis PE(20:0/22:1(13Z)) (PathBank: SMP0071787)
Phosphatidylethanolamine Biosynthesis PE(20:1(11Z)/20:1(11Z)) (PathBank: SMP0071788)
Phosphatidylethanolamine Biosynthesis PE(20:1(11Z)/20:1(13Z)) (PathBank: SMP0071789)
Phosphatidylethanolamine Biosynthesis PE(20:1(11Z)/22:0) (PathBank: SMP0071790)
Phosphatidylethanolamine Biosynthesis PE(20:1(11Z)/22:1(13Z)) (PathBank: SMP0071791)
Phosphatidylethanolamine Biosynthesis PE(20:1(13Z)/20:1(13Z)) (PathBank: SMP0071792)
Phosphatidylethanolamine Biosynthesis PE(20:1(13Z)/22:0) (PathBank: SMP0071793)
Phosphatidylethanolamine Biosynthesis PE(20:1(13Z)/22:1(13Z)) (PathBank: SMP0071794)
Phosphatidylethanolamine Biosynthesis PE(22:0/22:0) (PathBank: SMP0071795)
Phosphatidylethanolamine Biosynthesis PE(22:0/22:1(13Z)) (PathBank: SMP0071796)
Phosphatidylethanolamine Biosynthesis PE(22:1(13Z)/22:1(13Z)) (PathBank: SMP0071797)
L-Homomethionine Biosynthesis (PathBank: SMP0121204)

Rheumatoid arthritis (HMDB: HMDB0001491)

Disease pathway

Primary Hyperoxaluria Type I (PathBank: SMP0000352)
Pyruvate Carboxylase Deficiency (PathBank: SMP0000350)
beta-Ketothiolase Deficiency (PathBank: SMP0000173)
2-Methyl-3-hydroxybutryl-CoA Dehydrogenase Deficiency (PathBank: SMP0000137)
Propionic Acidemia (PathBank: SMP0000236)
3-Hydroxy-3-methylglutaryl-CoA Lyase Deficiency (PathBank: SMP0000138)
Maple Syrup Urine Disease (PathBank: SMP0000199)
3-Methylcrotonyl-CoA Carboxylase Deficiency Type I (PathBank: SMP0000237)
3-Methylglutaconic Aciduria Type I (PathBank: SMP0000139)
3-Methylglutaconic Aciduria Type III (PathBank: SMP0000140)
Methylmalonate Semialdehyde Dehydrogenase Deficiency (PathBank: SMP0000384)
Methylmalonic Aciduria (PathBank: SMP0000200)
4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase Deficiency (PathBank: SMP0000243)
Homocarnosinosis (PathBank: SMP0000385)
Hyperinsulinism-Hyperammonemia Syndrome (PathBank: SMP0000339)
Prolidase Deficiency (PD) (PathBank: SMP0000207)
Arginine: Glycine Amidinotransferase Deficiency (AGAT Deficiency) (PathBank: SMP0000362)
Hyperprolinemia Type II (PathBank: SMP0000360)
Hyperprolinemia Type I (PathBank: SMP0000361)
Prolinemia Type II (PathBank: SMP0000208)
Guanidinoacetate Methyltransferase Deficiency (GAMT Deficiency) (PathBank: SMP0000188)
Ornithine Aminotransferase Deficiency (OAT Deficiency) (PathBank: SMP0000363)
Aromatic L-Aminoacid Decarboxylase Deficiency (PathBank: SMP0000170)
Isovaleric Aciduria (PathBank: SMP0000238)
Canavan Disease (PathBank: SMP0000175)
Hypoacetylaspartia (PathBank: SMP0000192)
Cystathionine beta-Synthase Deficiency (PathBank: SMP0000177)
Hypermethioninemia (PathBank: SMP0000341)
S-Adenosylhomocysteine (SAH) Hydrolase Deficiency (PathBank: SMP0000214)
Glycine N-Methyltransferase Deficiency (PathBank: SMP0000222)
Methylenetetrahydrofolate Reductase Deficiency (MTHFRD) (PathBank: SMP0000340)
Methionine Adenosyltransferase Deficiency (PathBank: SMP0000221)
GABA-Transaminase Deficiency (PathBank: SMP0000351)
Glutaric Aciduria Type I (PathBank: SMP0000186)
Saccharopinuria/Hyperlysinemia II (PathBank: SMP0000239)
Histidinemia (PathBank: SMP0000191)
Lactic Acidemia (PathBank: SMP0000313)
Phenylketonuria (PathBank: SMP0000206)
Tyrosinemia Type 2 (or Richner-Hanhart Syndrome) (PathBank: SMP0000369)
Tyrosinemia Type 3 (TYRO3) (PathBank: SMP0000370)
Acute Intermittent Porphyria (PathBank: SMP0000344)
Porphyria Variegata (PV) (PathBank: SMP0000346)
Congenital Erythropoietic Porphyria (CEP) or Gunther Disease (PathBank: SMP0000345)
Alkaptonuria (PathBank: SMP0000169)
Hawkinsinuria (PathBank: SMP0000190)
Tyrosinemia Type I (PathBank: SMP0000218)
Argininemia (PathBank: SMP0000357)
Argininosuccinic Aciduria (PathBank: SMP0000003)
Citrullinemia Type I (PathBank: SMP0000001)
Ornithine Transcarbamylase Deficiency (OTC Deficiency) (PathBank: SMP0000205)
Carbamoyl Phosphate Synthetase Deficiency (PathBank: SMP0000002)
Dimethylglycine Dehydrogenase Deficiency (PathBank: SMP0000242)
Dihydropyrimidine Dehydrogenase Deficiency (DHPD) (PathBank: SMP0000179)
Sarcosinemia (PathBank: SMP0000244)
Gaucher Disease (PathBank: SMP0000349)
Globoid Cell Leukodystrophy (PathBank: SMP0000348)
Metachromatic Leukodystrophy (MLD) (PathBank: SMP0000347)
Malonic Aciduria (PathBank: SMP0000198)
Methylmalonic Aciduria Due to Cobalamin-Related Disorders (PathBank: SMP0000201)
Non-Ketotic Hyperglycinemia (PathBank: SMP0000223)
Hereditary Coproporphyria (HCP) (PathBank: SMP0000342)
2-Hydroxyglutric Aciduria (D and L Form) (PathBank: SMP0000136)
3-Methylglutaconic Aciduria Type IV (PathBank: SMP0000141)
Hyperglycinemia, Non-Ketotic (PathBank: SMP0000485)
Carnosinuria, Carnosinemia (PathBank: SMP0000493)
Tyrosinemia, Transient, of the Newborn (PathBank: SMP0000494)
Tyrosine Hydroxylase Deficiency (PathBank: SMP0000497)
Dopamine beta-Hydroxylase Deficiency (PathBank: SMP0000498)
beta-Mercaptolactate-Cysteine Disulfiduria (PathBank: SMP0000499)
Malonyl-CoA Decarboxylase Deficiency (PathBank: SMP0000502)
Hypophosphatasia (PathBank: SMP0000503)
Creatine Deficiency, Guanidinoacetate Methyltransferase Deficiency (PathBank: SMP0000504)
Hyperornithinemia with Gyrate Atrophy (HOGA) (PathBank: SMP0000505)
Hyperornithinemia-Hyperammonemia-Homocitrullinuria [HHH-syndrome] (PathBank: SMP0000506)
L-Arginine:Glycine Amidinotransferase Deficiency (PathBank: SMP0000507)
gamma-Cystathionase Deficiency (CTH) (PathBank: SMP0000514)
Homocystinuria, Cystathionine beta-Synthase Deficiency (PathBank: SMP0000515)
3-Hydroxyisobutyric Acid Dehydrogenase Deficiency (PathBank: SMP0000521)
3-Hydroxyisobutyric Aciduria (PathBank: SMP0000522)
Isobutyryl-CoA Dehydrogenase Deficiency (PathBank: SMP0000523)
Isovaleric Acidemia (PathBank: SMP0000524)
Fabry Disease (PathBank: SMP0000525)
Krabbe Disease (PathBank: SMP0000526)
Hyperlysinemia I, Familial (PathBank: SMP0000527)
Hyperlysinemia II or Saccharopinuria (PathBank: SMP0000528)
Monoamine Oxidase-A Deficiency (MAO-A) (PathBank: SMP0000533)
Glycogen Synthetase Deficiency (PathBank: SMP0000552)
Glycogenosis, Type III. Cori Disease, Debrancher Glycogenosis (PathBank: SMP0000553)
Glycogenosis, Type IV. Amylopectinosis, Anderson Disease (PathBank: SMP0000554)
Glycogenosis, Type VI. Hers Disease (PathBank: SMP0000555)
Mucopolysaccharidosis VI. Sly Syndrome (PathBank: SMP0000556)
Sucrase-Isomaltase Deficiency (PathBank: SMP0000557)
Succinic Semialdehyde Dehydrogenase Deficiency (PathBank: SMP0000567)
Homocystinuria-Megaloblastic Anemia Due to Defect in Cobalamin Metabolism, cblG Complementation Type (PathBank: SMP0000570)
Pyridoxine Dependency with Seizures (PathBank: SMP0000571)
2-Aminoadipic 2-Oxoadipic Aciduria (PathBank: SMP0000719)
3-Phosphoglycerate Dehydrogenase Deficiency (PathBank: SMP0000721)
Cystinosis, Ocular Nonnephropathic (PathBank: SMP0000722)
Folate Malabsorption, Hereditary (PathBank: SMP0000724)
Glutaminolysis and Cancer (PathBank: SMP0002298)
Sarcosine Oncometabolite Pathway (PathBank: SMP0002313)
2-Methyl-3-hydroxybutryl-CoA Dehydrogenase Deficiency (PathBank: SMP0120439)
Hyperornithinemia-Hyperammonemia-Homocitrullinuria [HHH-syndrome] (PathBank: SMP0120571)

Drug action pathway

Methotrexate Action Pathway (PathBank: SMP0000432)
Disulfiram Action Pathway (PathBank: SMP0000429)

Role

Industrial application

Pharmaceutical industry

Pharmaceutical (HMDB: HMDB0001491)

Biomarker

Rheumatoid arthritis (MarkerDB: MDB00000331)
Celiac disease (MarkerDB: MDB00000331)
Epilepsy (MarkerDB: MDB00000331)
Purine nucleoside phosphorylase deficiency (MarkerDB: MDB00000331)

Biological role

human metabolite (HMDB: HMDB0001491)
Escherichia coli metabolite (HMDB: HMDB0001491)
Saccharomyces cerevisiae metabolite (HMDB: HMDB0001491)
coenzyme (HMDB: HMDB0001491)

Modulator

Inhibitor

Enzyme inhibitor

EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor (HMDB: HMDB0001491)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	255 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	28 mg/mL	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Baker	150.538	30932474
[M-H]-	MetCCS_train_neg	146.336	30932474
[M+H]+	Baker	154.761	30932474
[M+H]+	MetCCS_train_pos	151.404	30932474
[M-H]-	Not Available	148.3	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000339
[M+H]+	Not Available	152.3	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000339

Predicted Molecular Properties

Property	Value	Source
Water Solubility	5.7 g/L	ALOGPS
logP	-0.55	ALOGPS
logP	-2.1	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.68	ChemAxon
pKa (Strongest Basic)	4.11	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	116.95 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	54.75 m³·mol⁻¹	ChemAxon
Polarizability	20.9 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	152.849	31661259
DarkChem	[M-H]-	149.58	31661259
AllCCS	[M+H]+	152.941	32859911
AllCCS	[M-H]-	147.71	32859911
DeepCCS	[M+H]+	147.643	30932474
DeepCCS	[M-H]-	145.285	30932474
DeepCCS	[M-2H]-	179.615	30932474
DeepCCS	[M+Na]+	154.766	30932474
AllCCS	[M+H]+	152.9	32859911
AllCCS	[M+H-H2O]+	149.2	32859911
AllCCS	[M+NH4]+	156.4	32859911
AllCCS	[M+Na]+	157.4	32859911
AllCCS	[M-H]-	147.7	32859911
AllCCS	[M+Na-2H]-	148.1	32859911
AllCCS	[M+HCOO]-	148.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pyridoxal 5'-phosphate	CC1=NC=C(COP(O)(O)=O)C(C=O)=C1O	2937.5	Standard polar	33892256
Pyridoxal 5'-phosphate	CC1=NC=C(COP(O)(O)=O)C(C=O)=C1O	1916.5	Standard non polar	33892256
Pyridoxal 5'-phosphate	CC1=NC=C(COP(O)(O)=O)C(C=O)=C1O	2191.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Pyridoxal 5'-phosphate,1TMS,isomer #1	CC1=NC=C(COP(=O)(O)O)C(C=O)=C1O[Si](C)(C)C	2203.8	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,1TMS,isomer #2	CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(C=O)=C1O	2183.0	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,2TMS,isomer #1	CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(C=O)=C1O[Si](C)(C)C	2256.0	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,2TMS,isomer #1	CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(C=O)=C1O[Si](C)(C)C	2134.1	Standard non polar	33892256
Pyridoxal 5'-phosphate,2TMS,isomer #1	CC1=NC=C(COP(=O)(O)O[Si](C)(C)C)C(C=O)=C1O[Si](C)(C)C	2835.0	Standard polar	33892256
Pyridoxal 5'-phosphate,2TMS,isomer #2	CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(C=O)=C1O	2195.9	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,2TMS,isomer #2	CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(C=O)=C1O	2144.7	Standard non polar	33892256
Pyridoxal 5'-phosphate,2TMS,isomer #2	CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(C=O)=C1O	2744.2	Standard polar	33892256
Pyridoxal 5'-phosphate,3TMS,isomer #1	CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(C=O)=C1O[Si](C)(C)C	2270.7	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,3TMS,isomer #1	CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(C=O)=C1O[Si](C)(C)C	2215.1	Standard non polar	33892256
Pyridoxal 5'-phosphate,3TMS,isomer #1	CC1=NC=C(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(C=O)=C1O[Si](C)(C)C	2487.5	Standard polar	33892256
Pyridoxal 5'-phosphate,1TBDMS,isomer #1	CC1=NC=C(COP(=O)(O)O)C(C=O)=C1O[Si](C)(C)C(C)(C)C	2478.3	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,1TBDMS,isomer #2	CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O	2420.3	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,2TBDMS,isomer #1	CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O[Si](C)(C)C(C)(C)C	2696.5	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,2TBDMS,isomer #1	CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O[Si](C)(C)C(C)(C)C	2562.4	Standard non polar	33892256
Pyridoxal 5'-phosphate,2TBDMS,isomer #1	CC1=NC=C(COP(=O)(O)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O[Si](C)(C)C(C)(C)C	3020.2	Standard polar	33892256
Pyridoxal 5'-phosphate,2TBDMS,isomer #2	CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O	2643.7	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,2TBDMS,isomer #2	CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O	2552.0	Standard non polar	33892256
Pyridoxal 5'-phosphate,2TBDMS,isomer #2	CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O	2949.6	Standard polar	33892256
Pyridoxal 5'-phosphate,3TBDMS,isomer #1	CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O[Si](C)(C)C(C)(C)C	2891.0	Semi standard non polar	33892256
Pyridoxal 5'-phosphate,3TBDMS,isomer #1	CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O[Si](C)(C)C(C)(C)C	2755.5	Standard non polar	33892256
Pyridoxal 5'-phosphate,3TBDMS,isomer #1	CC1=NC=C(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C(C=O)=C1O[Si](C)(C)C(C)(C)C	2790.4	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Pyridoxal 5'-phosphate GC-MS (1 MEOX; 3 TMS)	splash10-0gb9-2690000000-c9bacb7e657461e28407	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Pyridoxal 5'-phosphate GC-MS (Non-derivatized)	splash10-0gb9-2690000000-c9bacb7e657461e28407	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Pyridoxal 5'-phosphate GC-EI-TOF (Non-derivatized)	splash10-004j-0910000000-0408f3957221fc9882cd	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Pyridoxal 5'-phosphate GC-EI-TOF (Non-derivatized)	splash10-0gb9-1790000000-b01115fa8b4cfd3612c7	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pyridoxal 5'-phosphate GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9520000000-bfd574b2e5355694902a	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pyridoxal 5'-phosphate GC-MS (1 TMS) - 70eV, Positive	splash10-006t-9152000000-26c9f631195663322986	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pyridoxal 5'-phosphate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyridoxal 5'-phosphate Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-0f6t-0690000000-4aa57f3f28f0bdef9dcf	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyridoxal 5'-phosphate Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-0fxx-8900000000-ee972556340c61650528	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyridoxal 5'-phosphate Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-014l-9100000000-3cc29fb51820adecd59c	2012-07-24	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyridoxal 5'-phosphate LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negative-QTOF	splash10-0002-0090000000-9b86e80a9dd0de14ab59	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyridoxal 5'-phosphate LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negative-QTOF	splash10-03dj-9800000000-9313aa9cbf19bc6311c5	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Pyridoxal 5'-phosphate LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negative-QTOF	splash10-0002-9500000000-7ce120a58879e2214ce5	2012-08-31	HMDB team, MONA

Showing metabocard for Pyridoxal 5'-phosphate (HMDB0001491)

MOL for HMDB0001491 (Pyridoxal 5'-phosphate)

3D MOL for HMDB0001491 (Pyridoxal 5'-phosphate)

3D SDF for HMDB0001491 (Pyridoxal 5'-phosphate)

3D-SDF for HMDB0001491 (Pyridoxal 5'-phosphate)

PDB for HMDB0001491 (Pyridoxal 5'-phosphate)

3D PDB for HMDB0001491 (Pyridoxal 5'-phosphate)

SMILES for HMDB0001491 (Pyridoxal 5'-phosphate)

INCHI for HMDB0001491 (Pyridoxal 5'-phosphate)

Structure for HMDB0001491 (Pyridoxal 5'-phosphate)

3D Structure for HMDB0001491 (Pyridoxal 5'-phosphate)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra