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Human Metabolome Database Version 2.5

 

Showing metabocard for Pyridoxine 5'-phosphate (HMDB01319)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2005-11-16 15:48:42
Update Date 2009-05-05 20:58:43
Accession Number HMDB01319
Secondary Accession Numbers Not Available
Common Name Pyridoxine 5'-phosphate
Description Pyridoxine 5'-phosphate is a substrate for Pyridoxine-5'-phosphate oxidase and Pyridoxal kinase.
Synonyms
  1. 5-Hydroxy-4-(hydroxymethyl)-6-methyl-3-pyridylmethyl dihydrogen phosphate
  2. 5-hydroxy-6-methyl-3,4-Pyridinedimethanol alpha( 3)-(dihydrogen phosphate)
  3. Pyridoxine 5'-phosphate
  4. Pyridoxine 5'-phosphic acid
  5. Pyridoxine 5-phosphate
  6. Pyridoxine-5'-phosphate
  7. Pyridoxol 5-phosphate
  8. Pyridoxyl-5-phosphate
  9. pyridoxine-5P
  10. pyridoxine-P
  11. pyridoxine-phosphate
Chemical IUPAC Name [5-hydroxy-4-(hydroxymethyl)-6-methyl-pyridin-3-yl]methoxyphosphonic acid
Chemical Formula C8H12NO6P
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Heterocyclic molecules
Class
  • Pyridoxals and Derivatives
Sub Class
  • Pyridoxal phosphates
Family
  • Mammalian Metabolite
Species
  • primary alcohol
  • phenol or hydroxyhetarene
  • phosphoric acid ester
  • aromatic compound
  • heterocyclic compound
Biofunction
—
Application
—
Source
  • Endogenous
Average Molecular Weight 249.158
Monoisotopic Molecular Weight 249.040222
Isomeric SMILES CC1=NC=C(COP(O)(O)=O)C(CO)=C1O
Canonical SMILES CC1=NC=C(COP(O)(O)=O)C(CO)=C1O
KEGG Compound ID C00627 Link Image
BioCyc ID PYRIDOXINE-5P Link Image
BiGG ID 35527 Link Image
Wikipedia Link Not Available
NuGOwiki Link HMDB01319 Link Image
Metagene Link HMDB01319 Link Image
METLIN ID 6156 Link Image
PubChem Compound 1055 Link Image
PubChem Substance 8144282 Link Image
ChEBI ID Not Available
CAS Registry Number 447-05-2
InChI Identifier InChI=1/C8H12NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2,10-11H,3-4H2,1H3,(H2,12,13,14)
Synthesis Reference Argoudelis, Chris J. Preparation of crystalline pyridoxine 5'-phosphate and some of its properties. Journal of Agricultural and Food Chemistry (1986), 34(6), 995-8.
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 187.0 mg/mL [MEYLAN,WM et al. (1996)]; 9.41 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge -2
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -0.80 [Predicted by ALOGPS]; -1.7 [Predicted by PubChem via XLOGP]; -1.04 [MEYLAN,WM & HOWARD,PH (1995)] Calculated using ALOGPS
Material Safety Data Sheet (MSDS) Not Available
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID 1HO4 Link Image
Experimental PDB File Show
Experimental PDB Structure
Experimental 1H NMR Spectrum Not Available
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Not Available
Predicted 1H NMR Spectrum Show Image
Show Peaklist
Predicted 13C NMR Spectrum Show Image
Show Peaklist
Mass Spectrum Not Available
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • Cytoplasm (Predicted from LogP)
Biofluid Location
  • Blood
Tissue Location Not Available
Concentrations (Normal) Not Available
Concentrations (Abnormal)
Biofluid Blood
Value 0.003 (0.0-0.01) uM
Age Adult:>18 yrs old
Sex Female
Condition Obesity
Comments Not Available
References
  • Driskell JA, Chrisley BM, Reynolds LK, Moak SW: Plasma B6 vitamer and plasma and urinary 4-pyridoxic acid concentrations of middle-aged obese black women. J Chromatogr. 1991 Aug 23;568(2):333-40. [PubMed Link Image]
Associated Disorders
Condition References
Obesity
  • Driskell JA, Chrisley BM, Reynolds LK, Moak SW: Plasma B6 vitamer and plasma and urinary 4-pyridoxic acid concentrations of middle-aged obese black women. J Chromatogr. 1991 Aug 23;568(2):333-40. [PubMed Link Image]
OMIM ID
Pathways
Name SMPDB Link KEGG Link
Vitamin B6 Metabolism SMP00017 Link Image map00750 Link Image
General References Not Available
Metabolic Enzymes
  1. Pyridoxine-5'-phosphate oxidase
  2. Pyridoxal kinase
  3. Pyridoxal phosphate phosphatase
Enzyme 1 [top]
Enzyme 1 ID 5947
Enzyme 1 Name Pyridoxine-5'-phosphate oxidase
Enzyme 1 Synonyms
  1. Pyridoxamine-phosphate oxidase
Enzyme 1 Gene Name PNPO
Enzyme 1 Protein Sequence >Pyridoxine-5'-phosphate oxidase 
MTCWLRGVTATFGRPAEWPGYLSHLCGRSAAMDLGPMRKSYRGDREAFEETHLTSLDPVK
QFAAWFEEAVQCPDIGEANAMCLATCTRDGKPSARMLLLKGFGKDGFRFFTNFESRKGKE
LDSNPFASLVFYWEPLNRQVRVEGPVKKLPEEEAECYFHSRPKSSQIGAVVSHQSSVIPD
REYLRKKNEELEQLYQDQEVPKPKSWGGYVLYPQVMEFWQGQTNRLHDRIVFRRGLPTGD
SPLGPMTHRGEEDWLYERLAP
Enzyme 1 Number of Residues 261
Enzyme 1 Molecular Weight 29988
Enzyme 1 Theoretical pI 7.09
Enzyme 1 GO Classification
Function
  • FMN binding
  • binding
  • catalytic activity
  • nucleotide binding
  • oxidoreductase activity
  • oxidoreductase activity, acting on the CH-NH2 group of donors
  • oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
  • pyridoxamine-phosphate oxidase activity
Process
  • cellular metabolism
  • metabolism
  • physiological process
  • pyridoxine biosynthesis
  • pyridoxine metabolism
  • vitamin B6 metabolism
  • vitamin metabolism
  • water-soluble vitamin metabolism
Component
—
Enzyme 1 General Function Coenzyme transport and metabolism
Enzyme 1 Specific Function Oxidizes PNP and PMP into pyridoxal 5'-phosphate (PLP)
Enzyme 1 Pathways
Enzyme 1 Reactions
  • pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + ammonia + H2O2
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 21728336 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID Q9NVS9 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name PNPO_HUMAN Link Image
Enzyme 1 PDB ID 1NRG Link Image
Enzyme 1 PDB File Show
Enzyme 1 3D Structure
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >786 bp 
ATGACGTGCTGGCTGCGGGGCGTCACGGCGACGTTCGGGCGACCTGCCGAGTGGCCAGGC
TACCTCAGTCACCTGTGTGGTCGCAGTGCTGCCATGGACCTGGGACCCATGCGCAAGAGT
TACCGCGGGGACCGAGAGGCATTTGAGGAGACTCATCTGACCTCCCTTGACCCAGTGAAA
CAGTTTGCTGCCTGGTTTGAGGAGGCTGTTCAGTGTCCTGACATAGGGGAAGCCAATGCC
ATGTGTCTGGCTACCTGCACCAGAGATGGAAAACCCTCTGCTCGCATGTTGCTGCTGAAG
GGCTTCGGGAAAGATGGCTTCCGCTTCTTCACTAACTTCGAGAGTCGAAAAGGAAAAGAG
CTGGACTCTAATCCCTTTGCTTCCCTTGTCTTCTACTGGGAGCCACTTAACCGTCAGGTG
CGTGTGGAAGGCCCTGTGAAGAAACTGCCTGAGGAGGAGGCTGAGTGCTACTTCCACTCC
CGCCCCAAGAGCAGCCAGATTGGGGCTGTGGTCAGCCACCAGAGTTCTGTGATCCCTGAT
CGGGAGTATCTGAGAAAGAAAAATGAGGAACTGGAACAGCTCTACCAGGATCAAGAGGTG
CCCAAGCCAAAATCCTGGGGTGGCTATGTCCTGTACCCTCAGGTGATGGAGTTCTGGCAA
GGTCAAACCAACCGCCTGCATGACCGGATAGTCTTTCGGCGGGGCCTACCCACAGGAGAT
TCCCCTTTGGGGCCCATGACCCACCGCGGGGAGGAAGACTGGCTCTATGAGAGACTTGCA
CCTTAA
Enzyme 1 GenBank Gene ID AF468030 Link Image
Enzyme 1 GeneCard ID PNPO Link Image
Enzyme 1 GenAtlas ID PNPO Link Image
Enzyme 1 HGNC ID HGNC:30260 Link Image
Enzyme 1 Chromosome Location 17
Enzyme 1 Locus 17q21.32
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Musayev FN, Di Salvo ML, Ko TP, Schirch V, Safo MK: Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase. Protein Sci. 2003 Jul;12(7):1455-63. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 6344
Enzyme 2 Name Pyridoxal kinase
Enzyme 2 Synonyms
  1. Pyridoxine kinase
Enzyme 2 Gene Name PDXK
Enzyme 2 Protein Sequence >Pyridoxal kinase 
MEEECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSD
ELQELYEGLRLNNMNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKW
DGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGP
DTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAM
LLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKRDI
EDPEIVVQATVL
Enzyme 2 Number of Residues 312
Enzyme 2 Molecular Weight 35103
Enzyme 2 Theoretical pI 6.05
Enzyme 2 GO Classification
Function
  • catalytic activity
  • kinase activity
  • pyridoxal kinase activity
  • transferase activity
  • transferase activity, transferring phosphorus-containing groups
Process
—
Component
—
Enzyme 2 General Function Coenzyme transport and metabolism
Enzyme 2 Specific Function Required for synthesis of pyridoxal-5-phosphate from vitamin B6
Enzyme 2 Pathways
Enzyme 2 Reactions
  • ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 1946349 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID O00764 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name PDXK_HUMAN Link Image
Enzyme 2 PDB ID 1RFV Link Image
Enzyme 2 PDB File Show
Enzyme 2 3D Structure
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >939 bp 
ATGGAGGAGGAGTGCCGGGTGCTCTCCATACAGAGCCACGTCATCCGCGGCTACGTGGGC
AACCGGGCGGCCACGTTCCCGCTGCAGGTTTTGGGATTTGAGATTGACGCGGTGAACTCT
GTCCAGTTTTCAAACCACACAGGCTATGCCCACTGGAAGGGCCAAGTGCTGAATTCAGAT
GAGCTCCAGGAGTTGTACGAAGGCCTGAGGCTGAACAACATGAATAAATATGACTACGTG
CTCACAGGTTATACGAGGGACAAGTCGTTCCTGGCCATGGTGGTGGACATTGTGCAGGAG
CTGAAGCAGCAGAACCCCAGGCTGGTGTACGTGTGTGATCCAGTCTTGGGTGACAAGTGG
GACGGCGAAGGCTCGATGTACGTCCCGGAGGACCTCCTTCCCGTCTACAAAGAAAAAGTG
GTGCCGCTTGCAGACATTATCACGCCCAACCAGTTTGAGGCCGAGTTACTGAGTGGCCGG
AAGATCCACAGCCAGGAGGAAGCCTTGCGGGTGATGGACATGCTGCACTCTATGGGCCCC
GACACCGTGGTCATCACCAGCTCCGACCTGCCCTCCCCGCAGGGCAGCAACTACCTGATT
GTGCTGGGGAGTCAGAGGAGGAGGAATCCCGCTGGCTCCGTGGTGATGGAACGCATCCGG
ATGGACATTCGCAAAGTGGACGCCGTCTTTGTGGGCACTGGGGACCTGTTTGCTGCCATG
CTCCTGGCGTGGACACACAAGCACCCCAATAACCTCAAGGTGGCCTGTGAGAAGACCGTG
TCTACCTTGCACCACGTTCTGCAGAGGACCATCCAGTGTGCAAAAGCCCAGGCCGGGGAA
GGAGTGAGGCCCAGCCCCATGCAGCTGGAGCTGCGGATGGTGCAGAGCAAAAGGGACATC
GAGGACCCAGAGATCGTCGTCCAGGCCACGGTGCTGTGA
Enzyme 2 GenBank Gene ID U89606 Link Image
Enzyme 2 GeneCard ID PDXK Link Image
Enzyme 2 GenAtlas ID PDXK Link Image
Enzyme 2 HGNC ID HGNC:8819 Link Image
Enzyme 2 Chromosome Location Not Available
Enzyme 2 Locus Not Available
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. Hanna MC, Turner AJ, Kirkness EF: Human pyridoxal kinase. cDNA cloning, expression, and modulation by ligands of the benzodiazepine receptor. J Biol Chem. 1997 Apr 18;272(16):10756-60. [PubMed Link Image]
  2. Hattori M, Fujiyama A, Taylor TD, Watanabe H, Yada T, Park HS, Toyoda A, Ishii K, Totoki Y, Choi DK, Groner Y, Soeda E, Ohki M, Takagi T, Sakaki Y, Taudien S, Blechschmidt K, Polley A, Menzel U, Delabar J, Kumpf K, Lehmann R, Patterson D, Reichwald K, Rump A, Schillhabel M, Schudy A, Zimmermann W, Rosenthal A, Kudoh J, Schibuya K, Kawasaki K, Asakawa S, Shintani A, Sasaki T, Nagamine K, Mitsuyama S, Antonarakis SE, Minoshima S, Shimizu N, Nordsiek G, Hornischer K, Brant P, Scharfe M, Schon O, Desario A, Reichelt J, Kauer G, Blocker H, Ramser J, Beck A, Klages S, Hennig S, Riesselmann L, Dagand E, Haaf T, Wehrmeyer S, Borzym K, Gardiner K, Nizetic D, Francis F, Lehrach H, Reinhardt R, Yaspo ML: The DNA sequence of human chromosome 21. Nature. 2000 May 18;405(6784):311-9. [PubMed Link Image]
  3. Lee HS, Moon BJ, Choi SY, Kwon OS: Human pyridoxal kinase: overexpression and properties of the recombinant enzyme. Mol Cells. 2000 Aug 31;10(4):452-9. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available
Enzyme 3 [top]
Enzyme 3 ID 9426
Enzyme 3 Name Pyridoxal phosphate phosphatase
Enzyme 3 Synonyms
  1. PLP phosphatase
Enzyme 3 Gene Name PDXP
Enzyme 3 Protein Sequence >Pyridoxal phosphate phosphatase 
MARCERLRGAALRDVLGRAQGVLFDCDGVLWNGERAVPGAPELLERLARAGKAALFVSNN
SRRARPELALRFARLGFGGLRAEQLFSSALCAARLLRQRLPGPPDAPGAVFVLGGEGLRA
ELRAAGLRLAGDPSAGDGAAPRVRAVLVGYDEHFSFAKLREACAHLRDPECLLVATDRDP
WHPLSDGSRTPGTGSLAAAVETASGRQALVVGKPSPYMFECITENFSIDPARTLMVGDRL
ETDILFGHRCGMTTVLTLTGVSRLEEAQAYLAAGQHDLVPHYYVESIADLTEGLED
Enzyme 3 Number of Residues 296
Enzyme 3 Molecular Weight 31699
Enzyme 3 Theoretical pI Not Available
Enzyme 3 GO Classification
Function
  • catalytic activity
  • hydrolase activity
  • hydrolase activity, acting on ester bonds
  • phosphoric ester hydrolase activity
  • phosphoric monoester hydrolase activity
Process
  • metabolism
  • physiological process
Component
—
Enzyme 3 General Function Carbohydrate transport and metabolism
Enzyme 3 Specific Function Pyridoxal phosphate phosphatase. Has some activity towards pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PMP) and Pyridoxine 5'-phosphate (PNP), with a highest activity with PLP followed by PNP
Enzyme 3 Pathways
Enzyme 3 Reactions
  • H2O + Pyridoxamine 5'-phosphate --> Phosphate + Pyridoxamine
Enzyme 3 Pfam Domain Function
Enzyme 3 Signals
  • None
Enzyme 3 Transmembrane Regions
  • None
Enzyme 3 Essentiality Not Available
Enzyme 3 GenBank ID Protein 37545684 Link Image
Enzyme 3 UniProtKB/Swiss-Prot ID Q96GD0 Link Image
Enzyme 3 UniProtKB/Swiss-Prot Entry Name PLPP_HUMAN Link Image
Enzyme 3 PDB ID Not Available
Enzyme 3 Cellular Location Not Available
Enzyme 3 Gene Sequence Not Available
Enzyme 3 GenBank Gene ID AY125047 Link Image
Enzyme 3 GeneCard ID Not Available
Enzyme 3 GenAtlas ID PDXP Link Image
Enzyme 3 HGNC ID HGNC:30259 Link Image
Enzyme 3 Chromosome Location Not Available
Enzyme 3 Locus Not Available
Enzyme 3 SNPs SNPJam Report Link Image
Enzyme 3 General References
  1. Dunham I, Shimizu N, Roe BA, Chissoe S, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida JP, Babbage A, Bagguley C, Bailey J, Barlow K, Bates KN, Beasley O, Bird CP, Blakey S, Bridgeman AM, Buck D, Burgess J, Burrill WD, O'Brien KP, et al.: The DNA sequence of human chromosome 22. Nature. 1999 Dec 2;402(6761):489-95. [PubMed Link Image]
Enzyme 3 Metabolite References Not Available