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Human Metabolome Database Version 2.5

 

Showing metabocard for Vitamin K1 2,3-epoxide (HMDB02972)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2006-05-22 16:12:23
Update Date 2010-07-22 17:52:19
Accession Number HMDB02972
Secondary Accession Numbers Not Available
Common Name Vitamin K1 2,3-epoxide
Description Vitamin K1 2,3-epoxide is a vitamin K derivative. Vitamin K needed for the posttranslational modification of certain proteins, mostly required for blood coagulation. Within the cell, Vitamin K undergoes electron reduction to a reduced form of Vitamin K (called Vitamin K hydroquinone) by the enzyme Vitamin K epoxide reductase (or VKOR). Another enzyme then oxidizes Vitamin K hydroquinone to allow carboxylation of Glutamate to Gamma-cabroxygluatmate (Gla); this enzyme is called the gamma-glutamyl carboxylase or the Vitamin K-dependent carboxylase. The carboxylation reaction will only proceed if the carboxylase enzyme is able to oxidize Vitamin K hydroquinone to vitamin K epoxide at the same time; the carboxylation and epoxidation reactions are said to be coupled reactions. Vitamin K epoxide is then re-converted to Vitamin K by the Vitamin K epoxide reductase. These two enzymes comprise the so-called Vitamin K cycle. One of the reasons why Vitamin K is rarely deficient in a human diet is because Vitamin K is continually recycled in our cells. Vitamin K 2,3-epoxide is the substrate for vitamin K 2,3-epoxide reductase (VKOR) complex. Significantly increased level of serum vitamin K epoxide has been found in patients with familial multiple coagulation factor deficiency. (PMID 12384421) Accumulation of vitamin K1-2,3-epoxide in plasma is also a sensitive marker of coumarin-like activity of drugs. (PMID 2401753)
Synonyms
  1. (2,3-Epoxyphytyl)menaquinone
  2. 2,3-Epoxyphylloquinone
  3. Phylloquinone 2,3-epoxide
  4. Phylloquinone-2,3-epoxide
  5. Vitamin K 2,3-epoxide
  6. Vitamin K epoxide
  7. Vitamin K1 oxide
  8. 2,3-epoxy-2,3-dihydro-2-methyl-3-phytyl-1,4-naphthoquinone
  9. 1,4-Naphthoquinone, 2,3-epoxy-2,3-dihydro-2-methyl-3-phytyl-2,3-Epoxyphylloquinone
  10. Naphth[2,3-b]oxirene-2,7-dione, 1a,7a-dihydro-1a-methyl-7a-(3,7,11,15-tetramethyl-2-hexadecenyl)-Phylloquinone oxide
Chemical IUPAC Name 1a-methyl-7a-(3,7,11,15-tetramethylhexadec-2-enyl)naphtho[2,3-b]oxirene-2,7-dione
Chemical Formula C31H46O3
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Ketones and aldehydes
Class
  • Naphthoquinones
  • Ketones
Sub Class
  • Short chain keto-acids
Family
  • Mammalian Metabolite
Species
  • ketone
  • dialkyl ether
  • alkene
  • aromatic compound
  • heterocyclic compound
Biofunction
—
Application
—
Source
  • Endogenous
Average Molecular Weight 466.695
Monoisotopic Molecular Weight 466.344696
Isomeric SMILES CC(C)CCCC(C)CCCC(C)CCCC(C)=CCC12OC1(C)C(=O)C1=CC=CC=C1C2=O
Canonical SMILES CC(C)CCCC(C)CCCC(C)CCCC(C)=CCC12OC1(C)C(=O)C1=CC=CC=C1C2=O
KEGG Compound ID C05849 Link Image
BioCyc ID 23-EPOXY-23-DIHYDRO-2-METHYL-14-NAPHTHOQ Link Image
BiGG ID Not Available
Wikipedia Link Not Available
NuGOwiki Link HMDB02972 Link Image
Metagene Link HMDB02972 Link Image
METLIN ID 3030 Link Image
PubChem Compound 91577 Link Image
PubChem Substance 11533142 Link Image
ChEBI ID 28371 Link Image
CAS Registry Number 25486-55-9
InChI Identifier InChI=1/C31H46O3/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-31-29(33)27-19-8-7-18-26(27)28(32)30(31,6)34-31/h7-8,18-20,22-24H,9-17,21H2,1-6H3
Synthesis Reference Not Available
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 2.24e-05 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity 8.28 [Predicted by ALOGPS]; 8.4 [Predicted by PubChem via XLOGP] 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 Not Available
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
  • Membrane (Predicted from LogP)
Biofluid Location
  • Blood
Tissue Location Not Available
Concentrations (Normal)
Biofluid Blood
Value 0.0000021 uM
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Hirauchi K, Sakano T, Nagaoka T, Morimoto A: Simultaneous determination of vitamin K1, vitamin K1 2,3-epoxide and menaquinone-4 in human plasma by high-performance liquid chromatography with fluorimetric detection. J Chromatogr. 1988 Aug 19;430(1):21-9. [PubMed Link Image]
Concentrations (Abnormal) Not Available
Associated Disorders Not Available
OMIM ID Not Available
Pathways
Name SMPDB Link KEGG Link
Vitamin K Metabolism SMP00464 Link Image
General References
  1. Komatsu K, Kayashima N, Ariyoshi N, Shirahata A: [Vitamin K] Nippon Rinsho. 1993 Apr;51(4):943-51. [PubMed Link Image]
  2. Hirauchi K, Sakano T, Nagaoka T, Morimoto A: Simultaneous determination of vitamin K1, vitamin K1 2,3-epoxide and menaquinone-4 in human plasma by high-performance liquid chromatography with fluorimetric detection. J Chromatogr. 1988 Aug 19;430(1):21-9. [PubMed Link Image]
  3. McBurney A, Shearer MJ, Barkhan P: Changes in the urinary metabolites of phylloquinone (vitamin K1) in man following therapeutic anticoagulation with warfarin. Biochem Pharmacol. 1978 Feb 1;27(3):273-8. [PubMed Link Image]
Metabolic Enzymes
  1. Vitamin K-dependent gamma-carboxylase
  2. Vitamin K epoxide reductase complex subunit 1
  3. Vitamin K epoxide reductase complex, subunit 1, isoform CRA_d
Enzyme 1 [top]
Enzyme 1 ID 7028
Enzyme 1 Name Vitamin K-dependent gamma-carboxylase
Enzyme 1 Synonyms
  1. Gamma-glutamyl carboxylase
  2. Vitamin K gamma glutamyl carboxylase
Enzyme 1 Gene Name GGCX
Enzyme 1 Protein Sequence >Vitamin K-dependent gamma-carboxylase 
MAVSAGSARTSPSSDKVQKDKAELISGPRQDSRIGKLLGFEWTDLSSWRRLVTLLNRPTD
PASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYT
IMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYW
SVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVKKLDADWVEGYSMEYLSRHWLFSP
FKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFS
YVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRH
QLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVHSRSHQHVKITYRDGRT
GELGYLNPGVFTQSRRWKDHADMLKQYATCLSRLLPKYNVTEPQIYFDIWVSINDRFQQR
IFDPRVDIVQAAWSPFQRTSWVQPLLMDLSPWRAKLQEIKSSLDNHTEVVFIADFPGLHL
ENFVSEDLGNTSIQLLQGEVTVELVAEQKNQTLREGEKMQLPAGEYHKVYTTSPSPSCYM
YVYVNTTELALEQDLAYLQELKEKVENGSETGPLPPELQPLLEGEVKGGPEPTPLVQTFL
RRQQRLQEIERRRNTPFHERFFRFLLRKLYVFRRSFLMTCISLRNLILGRPSLEQLAQEV
TYANLRPFEAVGELNPSNTDSSHSNPPESNPDPVHSEF
Enzyme 1 Number of Residues 758
Enzyme 1 Molecular Weight 87562
Enzyme 1 Theoretical pI 8.10
Enzyme 1 GO Classification
Function
  • carbon-carbon lyase activity
  • carboxy-lyase activity
  • catalytic activity
  • gamma-glutamyl carboxylase activity
  • lyase activity
Process
  • biopolymer metabolism
  • biopolymer modification
  • macromolecule metabolism
  • metabolism
  • peptidyl-amino acid modification
  • peptidyl-glutamic acid carboxylation
  • peptidyl-glutamic acid modification
  • physiological process
  • protein modification
Component
—
Enzyme 1 General Function Not Available
Enzyme 1 Specific Function Mediates the vitamin K-dependent carboxylation of glutamate residues to calcium binding gamma-carboxyglutamate (Gla) residues with the concomitant convertion of the reduced hydroquinone form of vitamin K to vitamin K epoxide
Enzyme 1 Pathways Not Available
Enzyme 1 Reactions Not Available
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • 61-81 114-134 137-157 293-313 362-382
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 184028 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P38435 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name VKGC_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >2277 bp 
ATGGCGGTGTCTGCCGGGTCCGCGCGGACCTCGCCCAGCTCAGATAAAGTACAGAAAGAC
AAGGCTGAACTGATCTCAGGGCCCAGGCAGGACAGCCGAATAGGGAAACTCTTGGGTTTT
GAGTGGACAGATTTGTCCAGTTGGCGGAGGCTGGTGACCCTGCTGAATCGACCAACGGAC
CCTGCAAGCTTAGCTGTCTTTCGTTTTCTTTTTGGGTTCTTGATGGTGCTAGACATTCCC
CAGGAGCGGGGGCTCAGCTCTCTGGACCGGAAATACCTTGATGGGCTGGATGTGTGCCGC
TTCCCCTTGCTGGATGCCCTACGCCCACTGCCACTTGACTGGATGTATCTTGTCTACACC
ATCATGTTTCTGGGGGCACTGGGCATGATGCTGGGCCTGTGCTACCGGATAAGCTGTGTG
TTATTCCTGCTGCCATACTGGTATGTGTTTCTCCTGGACAAGACATCATGGAACAACCAC
TCCTATCTGTATGGGTTGTTGGCCTTTCAGCTAACATTCATGGATGCAAACCACTACTGG
TCTGTGGACGGTCTGCTGAATGCCCATAGGAGGAATGCCCACGTGCCCCTTTGGAACTAT
GCAGTGCTCCGTGGCCAGATCTTCATTGTGTACTTCATTGCGGGTGTGAAAAAGCTGGAT
GCAGACTGGGTTGAAGGCTATTCCATGGAATATTTGTCCCGGCACTGGCTCTTCAGTCCC
TTCAAACTGCTGTTGTCTGAGGAGCTGACTAGCCTGCTGGTCGTGCACTGGGGTGGGCTG
CTGCTTGACCTCTCAGCTGGTTTCCTGCTCTTTTTTGATGTCTCAAGATCCATTGGCCTG
TTCTTTGTGTCCTACTTCCACTGCATGAATTCCCAGCTTTTCAGCATTGGTATGTTCTCC
TACGTCATGCTGGCCAGCAGCCCTCTCTTCTGCTCCCCTGAGTGGCCTCGGAAGCTGGTG
TCCTACTGCCCCCAAAGGTTGCAACAACTGTTGCCCCTCAAGGCAGCCCCTCAGCCCAGT
GTTTCCTGTGTGTATAAGAGGAGCCGGGGCAAAAGTGGCCAGAAGCCAGGGCTGCGCCAT
CAGCTGGGAGCTGCCTTCACCCTGCTCTACCTCCTGGAGCAGCTATTCCTGCCCTATTCT
CATTTTCTCACCCAGGGCTATAACAACTGGACAAATGGGCTGTATGGCTATTCCTGGGAC
ATGATGGTGCACTCCCGTTCCCACCAGCACGTGAAGATCACCTACCGTGATGGCCGCACT
GGCGAACTGGGCTACCTTAACCCTGGGGTATTTACACAGAGTCGGCGATGGAAGGATCAT
GCAGACATGCTGAAGCAATATGCCACTTGCCTGAGCCGCCTGCTTCCCAAGTATAATGTC
ACTGAGCCCCAGATCTACTTTGATATTTGGGTCTCCATCAATGACCGCTTCCAGCAGAGG
ATTTTTGACCCTCGTGTGGACATCGTGCAGGCCGCTTGGTCACCCTTTCAGCGCACATCC
TGGGTGCAACCACTCTTGATGGACCTGTCTCCCTGGAGGGCCAAGTTACAGGAAATCAAG
AGCAGCCTAGACAACCACACTGAGGTGGTCTTCATTGCAGATTTCCCTGGACTGCACTTG
GAGAATTTTGTGAGTGAAGACCTGGGCAACACTAGCATCCAGCTGCTGCAGGGGGAAGTG
ACTGTGGAGCTTGTGGCAGAACAGAAGAACCAGACTCTTCGAGAGGGAGAAAAAATGCAG
TTGCCTGCTGGTGAGTACCATAAGGTGTATACGACATCACCTAGCCCTTCTTGCTACATG
TACGTCTATGTCAACACTACAGAGCTTGCACTGGAGCAAGACCTGGCATATCTGCAAGAA
TTAAAGGAAAAGGTGGAGAATGGAAGTGAAACAGGGCCTCTACCCCCAGAGCTGCAGCCT
CTGTTGGAAGGGGAAGTAAAAGGGGGCCCTGAGCCAACACCTCTGGTTCAGACCTTTCTT
AGACGCCAACAAAGGCTCCAGGAGATTGAACGCCGGCGAAATACTCCTTTCCATGAGCGA
TTCTTCCGCTTCTTGTTGCGAAAGCTCTATGTCTTTCGCCGCAGCTTCCTGATGACTTGT
ATCTCACTTCGAAATCTGATATTAGGCCGTCCTTCCCTGGAGCAGCTGGCCCAGGAGGTG
ACTTATGCAAACTTGAGACCCTTTGAGGCAGTTGGAGAACTGAATCCCTCAAACACGGAT
TCTTCACATTCTAATCCTCCTGAGTCAAATCCTGATCCTGTCCACTCAGAGTTCTGA
Enzyme 1 GenBank Gene ID M81592 Link Image
Enzyme 1 GeneCard ID GGCX Link Image
Enzyme 1 GenAtlas ID GGCX Link Image
Enzyme 1 HGNC ID HGNC:4247 Link Image
Enzyme 1 Chromosome Location 2
Enzyme 1 Locus 2p12
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Wu SM, Cheung WF, Frazier D, Stafford DW: Cloning and expression of the cDNA for human gamma-glutamyl carboxylase. Science. 1991 Dec 13;254(5038):1634-6. [PubMed Link Image]
  2. Wu SM, Stafford DW, Frazier LD, Fu YY, High KA, Chu K, Sanchez-Vega B, Solera J: Genomic sequence and transcription start site for the human gamma-glutamyl carboxylase. Blood. 1997 Jun 1;89(11):4058-62. [PubMed Link Image]
  3. Brenner B, Sanchez-Vega B, Wu SM, Lanir N, Stafford DW, Solera J: A missense mutation in gamma-glutamyl carboxylase gene causes combined deficiency of all vitamin K-dependent blood coagulation factors. Blood. 1998 Dec 15;92(12):4554-9. [PubMed Link Image]
  4. Spronk HM, Farah RA, Buchanan GR, Vermeer C, Soute BA: Novel mutation in the gamma-glutamyl carboxylase gene resulting in congenital combined deficiency of all vitamin K-dependent blood coagulation factors. Blood. 2000 Nov 15;96(10):3650-2. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 7727
Enzyme 2 Name Vitamin K epoxide reductase complex subunit 1
Enzyme 2 Synonyms
  1. Vitamin K1 2,3-epoxide reductase subunit 1
Enzyme 2 Gene Name VKORC1
Enzyme 2 Protein Sequence >Vitamin K epoxide reductase complex subunit 1 
MGSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWG
RGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAGSVYL
AWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQEPQGKAKRH
Enzyme 2 Number of Residues 163
Enzyme 2 Molecular Weight 18235
Enzyme 2 Theoretical pI 9.58
Enzyme 2 GO Classification Not Available
Enzyme 2 General Function Not Available
Enzyme 2 Specific Function Involved in vitamin K metabolism. Catalytic subunit of the vitamin K epoxide reductase (VKOR) complex which reduces inactive vitamin K 2,3-epoxide to active vitamin K
Enzyme 2 Pathways
Enzyme 2 Reactions
  • 2-methyl-3-phytyl-1,4-naphthoquinone + oxidized dithiothreitol + H2O = 2,3-epoxy-2,3-dihydro-2-methyl-3-phytyl-1,4-naphthoquinone + 1,4-dithiothreitol
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • 1-31
Enzyme 2 Transmembrane Regions Not Available
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 40217983 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID Q9BQB6 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name VKOR1_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >492 bp 
ATGGGCAGCACCTGGGGGAGCCCTGGCTGGGTGCGGCTCGCTCTTTGCCTGACGGGCTTA
GTGCTCTCGCTCTACGCGCTGCACGTGAAGGCGGCGCGCGCCCGGGACCGGGATTACCGC
GCGCTCTGCGACGTGGGCACCGCCATCAGCTGTTCGCGCGTCTTCTCCTCCAGGTGGGGC
AGGGGTTTCGGGCTGGTGGAGCATGTGCTGGGACAGGACAGCATCCTCAATCAATCCAAC
AGCATATTCGGTTGCATCTTCTACACACTACAGCTATTGTTAGGTTGCCTGCGGACACGC
TGGGCCTCTGTCCTGATGCTGCTGAGCTCCCTGGTGTCTCTCGCTGGTTCTGTCTACCTG
GCCTGGATCCTGTTCTTCGTGCTCTATGATTTCTGCATTGTTTGTATCACCACCTATGCT
ATCAACGTGAGCCTGATGTGGCTCAGTTTCCGGAAGGTCCAAGAACCCCAGGGCAAGGCT
AAGAGGCACTGA
Enzyme 2 GenBank Gene ID AY423044 Link Image
Enzyme 2 GeneCard ID VKORC1 Link Image
Enzyme 2 GenAtlas ID VKORC1 Link Image
Enzyme 2 HGNC ID HGNC:23663 Link Image
Enzyme 2 Chromosome Location 16
Enzyme 2 Locus 16p11.2
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. Clark HF, Gurney AL, Abaya E, Baker K, Baldwin D, Brush J, Chen J, Chow B, Chui C, Crowley C, Currell B, Deuel B, Dowd P, Eaton D, Foster J, Grimaldi C, Gu Q, Hass PE, Heldens S, Huang A, Kim HS, Klimowski L, Jin Y, Johnson S, Lee J, Lewis L, Liao D, Mark M, Robbie E, Sanchez C, Schoenfeld J, Seshagiri S, Simmons L, Singh J, Smith V, Stinson J, Vagts A, Vandlen R, Watanabe C, Wieand D, Woods K, Xie MH, Yansura D, Yi S, Yu G, Yuan J, Zhang M, Zhang Z, Goddard A, Wood WI, Godowski P, Gray A: The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Genome Res. 2003 Oct;13(10):2265-70. Epub 2003 Sep 15. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available
Enzyme 3 [top]
Enzyme 3 ID 16783
Enzyme 3 Name Vitamin K epoxide reductase complex, subunit 1, isoform CRA_d
Enzyme 3 Synonyms
  1. SubName: cDNA, FLJ92279
Enzyme 3 Gene Name VKORC1
Enzyme 3 Protein Sequence >Vitamin K epoxide reductase complex, subunit 1, isoform CRA_d 
MGSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWG
RGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAGSVYL
AWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQEPQGKAKRH
Enzyme 3 Number of Residues 163
Enzyme 3 Molecular Weight 18235
Enzyme 3 Theoretical pI 9.58
Enzyme 3 GO Classification Not Available
Enzyme 3 General Function Not Available
Enzyme 3 Specific Function Not Available
Enzyme 3 Pathways Not Available
Enzyme 3 Reactions Not Available
Enzyme 3 Pfam Domain Function
Enzyme 3 Signals
  • None
Enzyme 3 Transmembrane Regions
  • None
Enzyme 3 Essentiality Not Available
Enzyme 3 GenBank ID Protein Not Available
Enzyme 3 UniProtKB/Swiss-Prot ID B2R4Z6 Link Image
Enzyme 3 UniProtKB/Swiss-Prot Entry Name B2R4Z6_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 AK312005 Link Image
Enzyme 3 GeneCard ID B2R4Z6 Link Image
Enzyme 3 GenAtlas ID Not Available
Enzyme 3 HGNC ID Not Available
Enzyme 3 Chromosome Location 16
Enzyme 3 Locus 16p11.2
Enzyme 3 SNPs SNPJam Report Link Image
Enzyme 3 General References Not Available
Enzyme 3 Metabolite References Not Available