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Showing metabocard for Demethylphylloquinone (HMDB0004649)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-08-13 23:06:49 UTC
Update Date2022-03-07 02:49:21 UTC
HMDB IDHMDB0004649
Secondary Accession Numbers
  • HMDB04649
Metabolite Identification
Common NameDemethylphylloquinone
DescriptionDemethylphylloquinone is a form of vitamin K that occurs in nature as part of a series of compounds with a common 2-methyl-1,4 naphthoquinone nucleus and differing isoprenoid side chains at the 3 position. Vitamin K forms comprise a single major plant form, phylloquinone with a phytyl side chain and a family of bacterially synthesized menaquinones (MKs) with multiprenyl side chains. Bacterially produced menaquinones are biologically active forms of vitamin K that are present in high concentrations in the human lower bowel. Both phylloquinone and menaquinones are bioactive in hepatic gamma-carboxylation but long-chain MKs are less well absorbed. Liver stores of vitamin K are relatively small. The hepatic reserves of phylloquinone (approximately 10% of the total) are labile and turn over at a faster rate than menaquinones. Vitamin K is recognised as a factor required for normal blood coagulation, and in relation to its role in bone metabolism. Vitamin K is a substrate for a liver microsomal enzyme that catalyzes the conversion of specific glutamyl residues to gamma-carboxyglutamyl residues in a limited number of proteins. These include the vitamin K-dependent clotting factors: prothrombin (factor II), factor VII, factor IX, and factor X. In the absence of vitamin K, nonfunctional clotting factors are synthesized and hemorrhage can result. Vitamin K is a coenzyme for glutamate carboxylase, which mediates the conversion of glutamate to gamma-carboxyglutamate (Gla). There are at least three Gla proteins associated with bone tissue, of which osteocalcin is the most abundant and best known. Trabecular and cortical bone appear to contain substantial concentrations of both phylloquinone and menaquinones. (PMID: 8642453 , 8527227 , 15018483 , 1573141 ).
Structure
Data?1599944340
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0004649 (Demethylphylloquinone)


  Mrv1652309122022562D          

 32 33  0  0  0  0            999 V2000
 9966.5115 9973.1341    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9967.9370 9972.3094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9968.6506 9971.8950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9966.5115 9969.8260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 9972.2191 9972.3094    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9972.9325 9971.8950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9972.2191 9973.1341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 26 29  2  0  0  0  0
 23 28  2  0  0  0  0
M  END
Download

3D MOL for HMDB0004649 (Demethylphylloquinone)

HMDB0004649
     RDKit          3D
Demethylphylloquinone
 76 77  0  0  0  0  0  0  0  0999 V2000
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M  END
Download

3D SDF for HMDB0004649 (Demethylphylloquinone)


  Mrv1652309122022562D          

 32 33  0  0  0  0            999 V2000
 9966.5115 9973.1341    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9967.9370 9972.3094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9968.6506 9971.8950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9966.5115 9969.8260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9969.3643 9972.3094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9970.0782 9971.8950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9969.3643 9973.1341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9970.7920 9972.3094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9971.5057 9971.8950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9972.2191 9972.3094    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9972.9325 9971.8950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
  1 27  2  0  0  0  0
 32  2  1  0  0  0  0
 30  4  2  0  0  0  0
 26 29  2  0  0  0  0
 23 28  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0004649

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(C)=C\CC1=CC(=O)C2=CC=CC=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H44O2/c1-22(2)11-8-12-23(3)13-9-14-24(4)15-10-16-25(5)19-20-26-21-29(31)27-17-6-7-18-28(27)30(26)32/h6-7,17-19,21-24H,8-16,20H2,1-5H3/b25-19+/t23-,24-/m1/s1

> <INCHI_KEY>
UDYIPZFWVJJQJF-KQPZCCJBSA-N

> <FORMULA>
C30H44O2

> <MOLECULAR_WEIGHT>
436.68

> <EXACT_MASS>
436.334130657

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
54.22633794501712

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-1,4-dihydronaphthalene-1,4-dione

> <ALOGPS_LOGP>
8.38

> <JCHEM_LOGP>
9.300895319

> <ALOGPS_LOGS>
-7.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.479469686844748

> <JCHEM_PKA_STRONGEST_BASIC>
-7.173838497036545

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
138.59969999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.71e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-phytyl-1,4-naphthoquinone

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0004649 (Demethylphylloquinone)

HMDB0004649
     RDKit          3D
Demethylphylloquinone
 76 77  0  0  0  0  0  0  0  0999 V2000
   -3.8844    1.0774   -0.0484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3222    0.0809    0.8761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0667   -0.6362    1.6682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5080   -0.6848    1.8689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4258   -0.0311    0.9642 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2194    0.9512    1.4136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1509    1.6179    0.5287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8943    2.5466    0.9594 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3089    1.2911   -0.8821 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2038    1.9398   -1.7074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3085    1.5824   -3.0418 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5021    0.5679   -3.5269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6139   -0.0703   -2.6919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4920    0.2712   -1.3517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5642   -0.3860   -0.4566 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8262   -1.3238   -0.9147 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8130   -0.0547    0.8326 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2943   -1.0854    1.7728 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2147   -1.1301    1.6780 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7394   -1.4710    0.3320 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3180   -2.8026   -0.1940 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2728   -1.2996    0.2303 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9739   -2.1744    1.1972 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4372   -2.2125    1.2194 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2562   -1.0345    1.4605 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0679   -0.2674    2.7107 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4253   -0.1016    0.2773 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2837    1.0565    0.6431 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5083    2.0589   -0.3947 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2087    1.6057   -1.6294 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3560    2.9053   -2.4869 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4691    0.6466   -2.4910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0400    0.7225   -1.0845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1093    1.9187   -0.2049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7062    1.6030    0.4227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4597   -1.3523    2.3201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8602   -1.7827    1.9342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7372   -0.3237    2.9132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1393    1.2329    2.4734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8286    2.7418   -1.2862 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0206    2.1092   -3.6685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5753    0.2857   -4.5521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0056   -0.8536   -3.1094 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3428    0.9109    1.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6017   -0.4015   -0.2228 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7404   -2.0887    1.5979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5622   -0.7935    2.8078 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6621   -0.1676    1.9952 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5832   -1.8921    2.4090 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3636   -0.7112   -0.4186 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1010   -3.1232   -0.9428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6308   -2.7546   -0.7923 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2943   -3.6049    0.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5361   -1.5847   -0.8000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3942   -0.2092    0.4443 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6375   -3.2336    0.9357 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5615   -2.0761    2.2478 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7246   -3.0665    1.9253 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7606   -2.6622    0.2165 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3470   -1.4698    1.5613 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0177    0.2142    3.0235 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3430    0.5833    2.5598 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7549   -0.8790    3.5813 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9947   -0.7197   -0.4710 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4967    0.2320   -0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7848    1.5679    1.5329 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2589    0.6951    1.0881 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0453    2.9791    0.0399 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4971    2.5136   -0.6515 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2361    1.2680   -1.4520 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3771    3.0218   -2.9900 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5274    3.7577   -1.8300 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1511    2.7103   -3.2286 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8812   -0.3899   -2.5121 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4977    1.0440   -3.5735 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3978    0.5949   -2.2863 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  2  0
  2 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 25 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 30 32  1  0
 15  5  1  0
 14  9  1  0
  1 33  1  0
  1 34  1  0
  1 35  1  0
  3 36  1  0
  4 37  1  0
  4 38  1  0
  6 39  1  0
 10 40  1  0
 11 41  1  0
 12 42  1  0
 13 43  1  0
 17 44  1  0
 17 45  1  0
 18 46  1  0
 18 47  1  0
 19 48  1  0
 19 49  1  0
 20 50  1  6
 21 51  1  0
 21 52  1  0
 21 53  1  0
 22 54  1  0
 22 55  1  0
 23 56  1  0
 23 57  1  0
 24 58  1  0
 24 59  1  0
 25 60  1  1
 26 61  1  0
 26 62  1  0
 26 63  1  0
 27 64  1  0
 27 65  1  0
 28 66  1  0
 28 67  1  0
 29 68  1  0
 29 69  1  0
 30 70  1  0
 31 71  1  0
 31 72  1  0
 31 73  1  0
 32 74  1  0
 32 75  1  0
 32 76  1  0
M  END
Download

PDB for HMDB0004649 (Demethylphylloquinone)

HEADER    PROTEIN                                 12-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-20         0                                  
HETATM    1  O   UNK     0    8604.1558616.517   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0    8606.8168614.978   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8608.1488614.204   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8604.1558610.342   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8609.4808614.978   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8610.8138614.204   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8609.4808616.517   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8612.1458614.978   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8613.4778614.204   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8614.8098614.978   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8616.1418614.204   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8614.8098616.517   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8617.4768614.978   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8618.8088614.204   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8620.1438614.978   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8621.4758614.204   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8620.1438616.517   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8622.8068614.978   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8624.1428614.204   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0    8625.4748614.978   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8626.8058614.204   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8625.4748616.517   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8601.4958614.966   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0    8600.1658614.198   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0    8600.1658612.662   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0    8601.4958611.894   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0    8604.1548614.966   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0    8602.8248614.198   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0    8602.8248612.662   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0    8604.1548611.895   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0    8605.4848612.662   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0    8605.4848614.198   0.000  0.00  0.00           C+0
CONECT    1   27                                                            
CONECT    2    3   32                                                       
CONECT    3    2    5                                                       
CONECT    4   30                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5    8                                                       
CONECT    7    5                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10   13                                                       
CONECT   12   10                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15   18                                                       
CONECT   17   15                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   24   28                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   29                                                       
CONECT   27   28   32    1                                                  
CONECT   28   27   29   23                                                  
CONECT   29   28   30   26                                                  
CONECT   30   29   31    4                                                  
CONECT   31   30   32                                                       
CONECT   32   27   31    2                                                  
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END
Download

3D PDB for HMDB0004649 (Demethylphylloquinone)

COMPND    HMDB0004649
HETATM    1  C1  UNL     1      -3.884   1.077  -0.048  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.322   0.081   0.876  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.067  -0.636   1.668  1.00  0.00           C  
HETATM    4  C4  UNL     1      -5.508  -0.685   1.869  1.00  0.00           C  
HETATM    5  C5  UNL     1      -6.426  -0.031   0.964  1.00  0.00           C  
HETATM    6  C6  UNL     1      -7.219   0.951   1.414  1.00  0.00           C  
HETATM    7  C7  UNL     1      -8.151   1.618   0.529  1.00  0.00           C  
HETATM    8  O1  UNL     1      -8.894   2.547   0.959  1.00  0.00           O  
HETATM    9  C8  UNL     1      -8.309   1.291  -0.882  1.00  0.00           C  
HETATM   10  C9  UNL     1      -9.204   1.940  -1.707  1.00  0.00           C  
HETATM   11  C10 UNL     1      -9.308   1.582  -3.042  1.00  0.00           C  
HETATM   12  C11 UNL     1      -8.502   0.568  -3.527  1.00  0.00           C  
HETATM   13  C12 UNL     1      -7.614  -0.070  -2.692  1.00  0.00           C  
HETATM   14  C13 UNL     1      -7.492   0.271  -1.352  1.00  0.00           C  
HETATM   15  C14 UNL     1      -6.564  -0.386  -0.457  1.00  0.00           C  
HETATM   16  O2  UNL     1      -5.826  -1.324  -0.915  1.00  0.00           O  
HETATM   17  C15 UNL     1      -1.813  -0.055   0.833  1.00  0.00           C  
HETATM   18  C16 UNL     1      -1.294  -1.085   1.773  1.00  0.00           C  
HETATM   19  C17 UNL     1       0.215  -1.130   1.678  1.00  0.00           C  
HETATM   20  C18 UNL     1       0.739  -1.471   0.332  1.00  0.00           C  
HETATM   21  C19 UNL     1       0.318  -2.803  -0.194  1.00  0.00           C  
HETATM   22  C20 UNL     1       2.273  -1.300   0.230  1.00  0.00           C  
HETATM   23  C21 UNL     1       2.974  -2.174   1.197  1.00  0.00           C  
HETATM   24  C22 UNL     1       4.437  -2.213   1.219  1.00  0.00           C  
HETATM   25  C23 UNL     1       5.256  -1.034   1.461  1.00  0.00           C  
HETATM   26  C24 UNL     1       5.068  -0.267   2.711  1.00  0.00           C  
HETATM   27  C25 UNL     1       5.425  -0.102   0.277  1.00  0.00           C  
HETATM   28  C26 UNL     1       6.284   1.056   0.643  1.00  0.00           C  
HETATM   29  C27 UNL     1       6.508   2.059  -0.395  1.00  0.00           C  
HETATM   30  C28 UNL     1       7.209   1.606  -1.629  1.00  0.00           C  
HETATM   31  C29 UNL     1       7.356   2.905  -2.487  1.00  0.00           C  
HETATM   32  C30 UNL     1       6.469   0.647  -2.491  1.00  0.00           C  
HETATM   33  H1  UNL     1      -4.040   0.722  -1.085  1.00  0.00           H  
HETATM   34  H2  UNL     1      -3.109   1.919  -0.205  1.00  0.00           H  
HETATM   35  H3  UNL     1      -4.706   1.603   0.423  1.00  0.00           H  
HETATM   36  H4  UNL     1      -3.460  -1.352   2.320  1.00  0.00           H  
HETATM   37  H5  UNL     1      -5.860  -1.783   1.934  1.00  0.00           H  
HETATM   38  H6  UNL     1      -5.737  -0.324   2.913  1.00  0.00           H  
HETATM   39  H7  UNL     1      -7.139   1.233   2.473  1.00  0.00           H  
HETATM   40  H8  UNL     1      -9.829   2.742  -1.286  1.00  0.00           H  
HETATM   41  H9  UNL     1     -10.021   2.109  -3.668  1.00  0.00           H  
HETATM   42  H10 UNL     1      -8.575   0.286  -4.552  1.00  0.00           H  
HETATM   43  H11 UNL     1      -7.006  -0.854  -3.109  1.00  0.00           H  
HETATM   44  H12 UNL     1      -1.343   0.911   1.051  1.00  0.00           H  
HETATM   45  H13 UNL     1      -1.602  -0.401  -0.223  1.00  0.00           H  
HETATM   46  H14 UNL     1      -1.740  -2.089   1.598  1.00  0.00           H  
HETATM   47  H15 UNL     1      -1.562  -0.794   2.808  1.00  0.00           H  
HETATM   48  H16 UNL     1       0.662  -0.168   1.995  1.00  0.00           H  
HETATM   49  H17 UNL     1       0.583  -1.892   2.409  1.00  0.00           H  
HETATM   50  H18 UNL     1       0.364  -0.711  -0.419  1.00  0.00           H  
HETATM   51  H19 UNL     1       1.101  -3.123  -0.943  1.00  0.00           H  
HETATM   52  H20 UNL     1      -0.631  -2.755  -0.792  1.00  0.00           H  
HETATM   53  H21 UNL     1       0.294  -3.605   0.559  1.00  0.00           H  
HETATM   54  H22 UNL     1       2.536  -1.585  -0.800  1.00  0.00           H  
HETATM   55  H23 UNL     1       2.394  -0.209   0.444  1.00  0.00           H  
HETATM   56  H24 UNL     1       2.638  -3.234   0.936  1.00  0.00           H  
HETATM   57  H25 UNL     1       2.562  -2.076   2.248  1.00  0.00           H  
HETATM   58  H26 UNL     1       4.725  -3.067   1.925  1.00  0.00           H  
HETATM   59  H27 UNL     1       4.761  -2.662   0.216  1.00  0.00           H  
HETATM   60  H28 UNL     1       6.347  -1.470   1.561  1.00  0.00           H  
HETATM   61  H29 UNL     1       6.018   0.214   3.023  1.00  0.00           H  
HETATM   62  H30 UNL     1       4.343   0.583   2.560  1.00  0.00           H  
HETATM   63  H31 UNL     1       4.755  -0.879   3.581  1.00  0.00           H  
HETATM   64  H32 UNL     1       5.995  -0.720  -0.471  1.00  0.00           H  
HETATM   65  H33 UNL     1       4.497   0.232  -0.176  1.00  0.00           H  
HETATM   66  H34 UNL     1       5.785   1.568   1.533  1.00  0.00           H  
HETATM   67  H35 UNL     1       7.259   0.695   1.088  1.00  0.00           H  
HETATM   68  H36 UNL     1       7.045   2.979   0.040  1.00  0.00           H  
HETATM   69  H37 UNL     1       5.497   2.514  -0.652  1.00  0.00           H  
HETATM   70  H38 UNL     1       8.236   1.268  -1.452  1.00  0.00           H  
HETATM   71  H39 UNL     1       6.377   3.022  -2.990  1.00  0.00           H  
HETATM   72  H40 UNL     1       7.527   3.758  -1.830  1.00  0.00           H  
HETATM   73  H41 UNL     1       8.151   2.710  -3.229  1.00  0.00           H  
HETATM   74  H42 UNL     1       6.881  -0.390  -2.512  1.00  0.00           H  
HETATM   75  H43 UNL     1       6.498   1.044  -3.573  1.00  0.00           H  
HETATM   76  H44 UNL     1       5.398   0.595  -2.286  1.00  0.00           H  
CONECT    1    2   33   34   35
CONECT    2    3    3   17
CONECT    3    4   36
CONECT    4    5   37   38
CONECT    5    6    6   15
CONECT    6    7   39
CONECT    7    8    8    9
CONECT    9   10   10   14
CONECT   10   11   40
CONECT   11   12   12   41
CONECT   12   13   42
CONECT   13   14   14   43
CONECT   14   15
CONECT   15   16   16
CONECT   17   18   44   45
CONECT   18   19   46   47
CONECT   19   20   48   49
CONECT   20   21   22   50
CONECT   21   51   52   53
CONECT   22   23   54   55
CONECT   23   24   56   57
CONECT   24   25   58   59
CONECT   25   26   27   60
CONECT   26   61   62   63
CONECT   27   28   64   65
CONECT   28   29   66   67
CONECT   29   30   68   69
CONECT   30   31   32   70
CONECT   31   71   72   73
CONECT   32   74   75   76
END
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SMILES for HMDB0004649 (Demethylphylloquinone)

CC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(C)=C\CC1=CC(=O)C2=CC=CC=C2C1=O
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INCHI for HMDB0004649 (Demethylphylloquinone)

InChI=1S/C30H44O2/c1-22(2)11-8-12-23(3)13-9-14-24(4)15-10-16-25(5)19-20-26-21-29(31)27-17-6-7-18-28(27)30(26)32/h6-7,17-19,21-24H,8-16,20H2,1-5H3/b25-19+/t23-,24-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
PHNQ CPDHMDB
2-Phytyl-1,4-naphthoquinoneHMDB
2-[(2E,7R,11R)-3,7,11,15-Tetramethyl-2-hexadecenyl]-1,4-naphthalenedioneHMDB
Nor-alpha-phylloquinoneHMDB
Nor-α-phylloquinoneHMDB
Norvitamin KHMDB
DemethylphylloquinoneChEBI
Chemical FormulaC30H44O2
Average Molecular Weight436.68
Monoisotopic Molecular Weight436.334130657
IUPAC Name2-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-1,4-dihydronaphthalene-1,4-dione
Traditional Name2-phytyl-1,4-naphthoquinone
CAS Registry Number34625-86-0
SMILES
CC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(C)=C\CC1=CC(=O)C2=CC=CC=C2C1=O
InChI Identifier
InChI=1S/C30H44O2/c1-22(2)11-8-12-23(3)13-9-14-24(4)15-10-16-25(5)19-20-26-21-29(31)27-17-6-7-18-28(27)30(26)32/h6-7,17-19,21-24H,8-16,20H2,1-5H3/b25-19+/t23-,24-/m1/s1
InChI KeyUDYIPZFWVJJQJF-KQPZCCJBSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as vitamin k compounds. These are quinone lipids containing a methylated naphthoquinone ring structure, and vary in the aliphatic side chain attached at the 3-position.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassQuinone and hydroquinone lipids
Direct ParentVitamin K compounds
Alternative Parents
Substituents
  • Diterpenoid
  • Naphthoquinone
  • Naphthalene
  • Aryl ketone
  • Quinone
  • Benzenoid
  • Ketone
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP8.719Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility3.7e-05 g/LALOGPS
logP8.38ALOGPS
logP9.3ChemAxon
logS-7.1ALOGPS
pKa (Strongest Acidic)12.48ChemAxon
pKa (Strongest Basic)-7.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area34.14 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity138.6 m³·mol⁻¹ChemAxon
Polarizability54.23 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+212.31530932474
DeepCCS[M-H]-209.95730932474
DeepCCS[M-2H]-242.84130932474
DeepCCS[M+Na]+218.83230932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
DemethylphylloquinoneCC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(C)=C\CC1=CC(=O)C2=CC=CC=C2C1=O4267.0Standard polar33892256
DemethylphylloquinoneCC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(C)=C\CC1=CC(=O)C2=CC=CC=C2C1=O3311.8Standard non polar33892256
DemethylphylloquinoneCC(C)CCC[C@@H](C)CCC[C@@H](C)CCC\C(C)=C\CC1=CC(=O)C2=CC=CC=C2C1=O3394.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Demethylphylloquinone GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Demethylphylloquinone GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Demethylphylloquinone 10V, Positive-QTOFsplash10-000i-0125900000-60ee1796aba3070aecfd2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Demethylphylloquinone 20V, Positive-QTOFsplash10-00di-4912000000-0c3cb0b67fd0cded41a82021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Demethylphylloquinone 40V, Positive-QTOFsplash10-05fr-2910000000-1f5a699bad595e9e17812021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Demethylphylloquinone 10V, Negative-QTOFsplash10-000i-0000900000-386f84e878751722959d2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Demethylphylloquinone 20V, Negative-QTOFsplash10-00dr-0900700000-4029e6872c46a289779a2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Demethylphylloquinone 40V, Negative-QTOFsplash10-0fl1-0968300000-5c6ffbc09a6370adf5ae2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023391
KNApSAcK IDNot Available
Chemspider ID26333244
KEGG Compound IDNot Available
BioCyc IDCPD-6947
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound56927684
PDB IDNot Available
ChEBI ID31087
Food Biomarker OntologyNot Available
VMH IDDMPHQNO
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Shearer MJ, Bach A, Kohlmeier M: Chemistry, nutritional sources, tissue distribution and metabolism of vitamin K with special reference to bone health. J Nutr. 1996 Apr;126(4 Suppl):1181S-6S. [PubMed:8642453 ]
  2. Suttie JW: The importance of menaquinones in human nutrition. Annu Rev Nutr. 1995;15:399-417. [PubMed:8527227 ]
  3. Bugel S: Vitamin K and bone health. Proc Nutr Soc. 2003 Nov;62(4):839-43. [PubMed:15018483 ]
  4. Suttie JW: Vitamin K and human nutrition. J Am Diet Assoc. 1992 May;92(5):585-90. [PubMed:1573141 ]