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Showing metabocard for Lacto-N-difucopentaose II (HMDB0001986)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:30 UTC
Update Date2021-09-14 15:18:17 UTC
HMDB IDHMDB0001986
Secondary Accession Numbers
  • HMDB01986
Metabolite Identification
Common NameLacto-N-difucopentaose II
DescriptionLacto-N-difucopentaose II is an oligosaccharide first isolated from human milk by recycling chromatography in 1988. Is resistant to enzymic hydrolysis in the gastrointestinal tract of the infant; it is postulated that they reach the large intestine where they serve as substrates for bacterial metabolism. Oligosaccharides in human milk represent a group of bioactive molecules that have evolved to be an abundant and diverse component of human milk, even though they have no direct nutritive value to the infant. (PMID 3274083 , 10837303 , 11787695 , 14530096 , 17002410 ).
Structure
Data?1582752222
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001986 (Lacto-N-difucopentaose II)


  Mrv0541 02231219182D          

 73 77  0  0  1  0            999 V2000
   14.0163  -12.0303    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.0163  -12.8553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.7307  -13.2678    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.4452  -12.8553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4452  -12.0303    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.7307  -11.6178    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.1597  -11.6178    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8741  -12.0303    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0001986 (Lacto-N-difucopentaose II)

HMDB0001986
     RDKit          3D
Lacto-N-difucopentaose II
133137  0  0  0  0  0  0  0  0999 V2000
   -0.9013    1.5507   -3.4065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1796    0.3896   -2.5532 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8305   -0.7502   -2.8957 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8546    0.5733   -1.3259 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1743   -0.5259   -0.4167 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6333   -0.1436    0.9427 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2872   -0.3397    1.1047 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3934    0.8454    1.3502 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0203    0.8340    2.7169 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1189    0.1382    3.5674 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3135    0.0894    2.7117 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4480   -0.8621    3.9116 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7559   -1.3935    3.8582 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5055   -0.6047    1.5299 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6866    0.3321    0.5120 C   0  0  1  0  0  0  0  0  0  0  0  0
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    4.3469    0.1195   -1.0946 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1471    0.6501   -2.4677 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6460   -0.3295   -3.3345 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3907    1.2209   -3.0949 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9615    2.2208   -2.3115 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3710   -1.0173   -0.9816 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -4.2271   -1.8082   -0.2142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1206   -2.1474   -1.2419 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.3982   -2.3688   -0.8175 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.3777   -3.8419    1.0845 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0832   -2.9336    1.8986 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2187   -4.7534   -1.2400 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.5074   -5.9511   -0.5871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7322   -4.6079   -1.4925 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9926   -4.7242   -0.3309 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5323   -3.2418   -2.0976 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.1094   -3.1532   -3.3622 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6069    2.3898   -3.1286 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1260    1.9614   -3.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0471    1.3446   -4.4904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1725    1.5160   -0.9853 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1603    1.8754    3.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0021   -0.7855    3.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1401    0.8637    2.8196 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7093   -1.6727    3.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0001986 (Lacto-N-difucopentaose II)


  Mrv0541 02231219182D          

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M  END
> <DATABASE_ID>
HMDB0001986

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](O[C@@H]1O[C@H](CO)[C@H](O)[C@]([H])(O[C@@H]2O[C@H](CO)[C@@H](O[C@]3([H])O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]3O)[C@H](O[C@]3([H])O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)[C@H]2NC(C)=O)[C@H]1O)([C@H](O)CO)[C@]([H])(O[C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O)[C@H](O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C38H65NO29/c1-9-18(48)22(52)25(55)35(59-9)64-29(12(46)4-40)30(13(47)5-41)65-38-28(58)33(21(51)15(7-43)62-38)68-34-17(39-11(3)45)32(67-37-27(57)24(54)20(50)14(6-42)61-37)31(16(8-44)63-34)66-36-26(56)23(53)19(49)10(2)60-36/h4,9-10,12-38,41-44,46-58H,5-8H2,1-3H3,(H,39,45)/t9-,10-,12+,13+,14+,15+,16+,17+,18+,19+,20-,21-,22+,23+,24-,25-,26-,27+,28+,29+,30+,31+,32+,33-,34-,35-,36-,37-,38-/m0/s1

> <INCHI_KEY>
QNSWVQWPVUZACH-ZQTNVGDNSA-N

> <FORMULA>
C38H65NO29

> <MOLECULAR_WEIGHT>
999.912

> <EXACT_MASS>
999.364225123

> <JCHEM_ACCEPTOR_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
93.60987819095843

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
18

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(2R,3R,4R,5S)-1,2,5-trihydroxy-6-oxo-4-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]acetamide

> <ALOGPS_LOGP>
-2.00

> <JCHEM_LOGP>
-10.616754051666668

> <ALOGPS_LOGS>
-0.89

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.681053585016564

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.344494954767036

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6786211379015414

> <JCHEM_POLAR_SURFACE_AREA>
482.38000000000005

> <JCHEM_REFRACTIVITY>
207.42600000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
19

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.28e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(2R,3R,4R,5S)-1,2,5-trihydroxy-6-oxo-4-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]acetamide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001986 (Lacto-N-difucopentaose II)

HMDB0001986
     RDKit          3D
Lacto-N-difucopentaose II
133137  0  0  0  0  0  0  0  0999 V2000
   -0.9013    1.5507   -3.4065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1796    0.3896   -2.5532 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8305   -0.7502   -2.8957 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8546    0.5733   -1.3259 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1743   -0.5259   -0.4167 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6333   -0.1436    0.9427 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2872   -0.3397    1.1047 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3934    0.8454    1.3502 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0203    0.8340    2.7169 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1189    0.1382    3.5674 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3135    0.0894    2.7117 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4480   -0.8621    3.9116 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7559   -1.3935    3.8582 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5055   -0.6047    1.5299 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6866    0.3321    0.5120 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1001   -0.3295   -0.6135 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3469    0.1195   -1.0946 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1471    0.6501   -2.4677 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6460   -0.3295   -3.3345 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3907    1.2209   -3.0949 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9615    2.2208   -2.3115 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3710   -1.0173   -0.9816 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6182   -0.6742   -1.4103 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5740   -0.5314   -0.3974 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.8494    0.8459   -0.3733 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0395    1.2178    0.1521 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.9509    2.6406    0.6626 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6120    0.2851    1.1952 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.8195    0.2298    2.3324 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8051   -1.0813    0.5763 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.5532   -2.0290    1.5837 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8349   -1.2786   -0.5948 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.5247   -0.8018   -1.7349 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8494   -2.2495   -1.6540 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5458   -2.4805   -1.1488 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6487   -3.4780   -1.3976 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7617   -3.6842   -1.8256 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4302    1.1101    0.3035 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6994    2.4657    0.1348 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3934   -0.7844    1.9257 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5513   -0.0040    2.1037 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.4970   -0.6217    3.1118 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5954    0.2580    3.1851 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2213    0.3035    0.8049 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1962    1.6319    0.4349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4614    2.1987    0.2789 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.6826    2.5452   -1.0483 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6322    3.5183   -1.2183 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.9995    3.1183   -0.7100 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2084    4.8716   -0.6537 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.3462    5.6319   -0.4182 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3800    4.6813    0.5934 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.6992    5.6804    1.4947 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6292    3.3311    1.2276 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.7054    3.1990    2.2620 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6891   -0.5511   -0.3339 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2271   -1.8082   -0.2142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1206   -2.1474   -1.2419 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.3982   -2.3688   -0.8175 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7148   -3.6181   -0.3745 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.3777   -3.8419    1.0845 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0832   -2.9336    1.8986 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2187   -4.7534   -1.2400 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.5074   -5.9511   -0.5871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7322   -4.6079   -1.4925 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9926   -4.7242   -0.3309 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5323   -3.2418   -2.0976 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.1094   -3.1532   -3.3622 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6069    2.3898   -3.1286 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1260    1.9614   -3.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0471    1.3446   -4.4904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1725    1.5160   -0.9853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7643   -1.4582   -0.8238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8480    0.9570    1.0559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    1.6530    1.3171 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1603    1.8754    3.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0021   -0.7855    3.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1401    0.8637    2.8196 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7093   -1.6727    3.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3672   -0.2707    4.8376 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4137   -0.7340    3.5476 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4843    1.0759    0.8001 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6377    0.9520   -0.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3464    1.4662   -2.4661 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7121   -0.0242   -4.2797 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1612    0.4680   -3.3391 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0693    1.7433   -4.0424 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2329    2.7979   -1.9147 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3619   -1.2184    0.1376 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1090   -0.7668    0.5852 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7984    1.2602   -0.6835 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0704    2.8184    1.3035 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9316    3.2940   -0.2588 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.9014    2.9182    1.1704 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6052    0.6592    1.5081 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3577    0.2583    3.1755 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8475   -1.1793    0.2480 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2955   -2.0937    2.2158 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7218   -2.3783   -0.6632 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1200   -1.5524   -2.0081 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7474   -2.1675   -2.7454 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9960   -2.9428   -1.8485 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2221   -4.2582   -0.7849 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9781    0.7824   -0.6772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9577    2.9467   -0.3252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1848    0.9440    2.5709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9992   -0.6305    4.0975 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8480   -1.6068    2.7867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9154    0.3102    4.1363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3120    0.0195    0.8882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2355    1.4094    0.5059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7439    3.6721   -2.3165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3507    3.9085    0.0168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0142    2.1125   -0.2546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7728    3.1172   -1.5090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5341    5.3342   -1.4033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2157    6.5337   -0.8392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2843    4.7218    0.3787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9509    6.5261    1.0352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6386    3.2685    1.7160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8319    3.9278    2.9175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1222   -0.1036   -1.2597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1547   -1.2420   -1.9217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8433   -3.6952   -0.4192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6760   -4.8519    1.4275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3148   -3.7092    1.3135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8384   -3.0506    2.8491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7286   -4.6514   -2.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4242   -5.8247   -0.1967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4152   -5.3776   -2.1994 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.4308   -3.0761   -2.1529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1983   -4.0853   -3.6993 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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 28 95  1  1
 29 96  1  0
 30 97  1  6
 31 98  1  0
 32 99  1  6
 33100  1  0
 34101  1  6
 35102  1  0
 36103  1  0
 38104  1  6
 39105  1  0
 41106  1  1
 42107  1  0
 42108  1  0
 43109  1  0
 44110  1  1
 46111  1  1
 48112  1  6
 49113  1  0
 49114  1  0
 49115  1  0
 50116  1  6
 51117  1  0
 52118  1  6
 53119  1  0
 54120  1  1
 55121  1  0
 56122  1  6
 58123  1  6
 60124  1  1
 61125  1  0
 61126  1  0
 62127  1  0
 63128  1  6
 64129  1  0
 65130  1  6
 66131  1  0
 67132  1  6
 68133  1  0
M  END
Download

PDB for HMDB0001986 (Lacto-N-difucopentaose II)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      26.164 -22.457   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      26.164 -23.997   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.497 -24.767   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      28.831 -23.997   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      28.831 -22.457   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.497 -21.687   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      30.165 -21.687   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      31.498 -22.457   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      31.498 -23.997   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      32.832 -24.767   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      34.166 -23.997   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      34.166 -22.457   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      32.832 -21.687   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      27.497 -20.147   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      24.830 -21.687   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      24.830 -24.767   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      27.497 -26.307   0.000  0.00  0.00           C+0
HETATM   18  H   UNK     0      30.165 -23.227   0.000  0.00  0.00           H+0
HETATM   19  C   UNK     0      32.832 -20.147   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      31.498 -19.377   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      35.499 -24.767   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      36.833 -23.997   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      30.165 -24.767   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      30.165 -29.155   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      28.831 -29.926   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      28.831 -31.466   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      30.165 -32.235   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      31.498 -31.466   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      31.498 -29.926   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      27.497 -32.235   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      26.164 -31.466   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      30.165 -33.775   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      32.832 -32.235   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      32.447 -29.387   0.000  0.00  0.00           O+0
HETATM   35  H   UNK     0      31.498 -28.386   0.000  0.00  0.00           H+0
HETATM   36  C   UNK     0      38.167 -24.767   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      39.500 -23.997   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      39.500 -22.457   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      38.167 -21.687   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      36.833 -22.457   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      38.167 -20.147   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      39.500 -19.377   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      40.834 -20.147   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      39.500 -17.837   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      38.167 -17.067   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      40.834 -17.067   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0      42.168 -17.837   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      42.168 -19.377   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0      40.834 -21.687   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      44.541 -20.339   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0      44.541 -21.879   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      45.875 -22.649   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      47.208 -21.879   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      47.208 -20.339   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      45.875 -19.569   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      45.875 -18.029   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      42.168 -22.457   0.000  0.00  0.00           O+0
HETATM   58  C   UNK     0      42.168 -20.917   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0      48.542 -19.569   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      48.542 -22.649   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0      45.875 -24.189   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      38.167 -26.307   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0      40.834 -24.767   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0      42.168 -23.997   0.000  0.00  0.00           O+0
HETATM   65  H   UNK     0      36.833 -25.537   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0      38.167 -18.607   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0      39.500 -20.917   0.000  0.00  0.00           H+0
HETATM   68  O   UNK     0      35.499 -21.687   0.000  0.00  0.00           O+0
HETATM   69  N   UNK     0      32.832 -26.307   0.000  0.00  0.00           N+0
HETATM   70  O   UNK     0      43.501 -21.687   0.000  0.00  0.00           O+0
HETATM   71  C   UNK     0      34.166 -27.077   0.000  0.00  0.00           C+0
HETATM   72  O   UNK     0      35.191 -26.461   0.000  0.00  0.00           O+0
HETATM   73  C   UNK     0      34.166 -28.155   0.000  0.00  0.00           C+0
CONECT    1    2    6   15                                                  
CONECT    2    1    3   16                                                  
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7   18                                             
CONECT    6    5    1   14                                                  
CONECT    7    5    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10   23                                                  
CONECT   10    9   11   69                                                  
CONECT   11   10   12   21                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8   19                                                  
CONECT   14    6                                                            
CONECT   15    1                                                            
CONECT   16    2                                                            
CONECT   17    3                                                            
CONECT   18    5                                                            
CONECT   19   13   20                                                       
CONECT   20   19                                                            
CONECT   21   11   22                                                       
CONECT   22   21   36   40   65                                             
CONECT   23    9   24                                                       
CONECT   24   23   25   29   35                                             
CONECT   25   24   26                                                       
CONECT   26   25   27   30                                                  
CONECT   27   26   28   32                                                  
CONECT   28   27   29   33                                                  
CONECT   29   28   24   34                                                  
CONECT   30   26   31                                                       
CONECT   31   30                                                            
CONECT   32   27                                                            
CONECT   33   28                                                            
CONECT   34   29                                                            
CONECT   35   24                                                            
CONECT   36   22   37   62                                                  
CONECT   37   36   38   63                                                  
CONECT   38   37   39                                                       
CONECT   39   38   40   41                                                  
CONECT   40   39   22   68                                                  
CONECT   41   39   42                                                       
CONECT   42   41   43   44   66                                             
CONECT   43   42   48   49   67                                             
CONECT   44   42   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44   47                                                       
CONECT   47   46                                                            
CONECT   48   43   50                                                       
CONECT   49   43   57   58                                                  
CONECT   50   48   51   55                                                  
CONECT   51   50   52                                                       
CONECT   52   51   53   61                                                  
CONECT   53   52   54   60                                                  
CONECT   54   53   55   59                                                  
CONECT   55   54   50   56                                                  
CONECT   56   55                                                            
CONECT   57   49                                                            
CONECT   58   49   70                                                       
CONECT   59   54                                                            
CONECT   60   53                                                            
CONECT   61   52                                                            
CONECT   62   36                                                            
CONECT   63   37   64                                                       
CONECT   64   63                                                            
CONECT   65   22                                                            
CONECT   66   42                                                            
CONECT   67   43                                                            
CONECT   68   40                                                            
CONECT   69   10   71                                                       
CONECT   70   58                                                            
CONECT   71   69   72   73                                                  
CONECT   72   71                                                            
CONECT   73   71                                                            
MASTER        0    0    0    0    0    0    0    0   73    0  154    0
END
Download

3D PDB for HMDB0001986 (Lacto-N-difucopentaose II)

COMPND    HMDB0001986
HETATM    1  C1  UNL     1      -0.901   1.551  -3.407  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.180   0.390  -2.553  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.831  -0.750  -2.896  1.00  0.00           O  
HETATM    4  N1  UNL     1      -1.855   0.573  -1.326  1.00  0.00           N  
HETATM    5  C3  UNL     1      -2.174  -0.526  -0.417  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.633  -0.144   0.943  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.287  -0.340   1.105  1.00  0.00           O  
HETATM    8  C5  UNL     1       0.393   0.845   1.350  1.00  0.00           C  
HETATM    9  C6  UNL     1       1.020   0.834   2.717  1.00  0.00           C  
HETATM   10  O3  UNL     1       0.119   0.138   3.567  1.00  0.00           O  
HETATM   11  C7  UNL     1       2.314   0.089   2.712  1.00  0.00           C  
HETATM   12  C8  UNL     1       2.448  -0.862   3.912  1.00  0.00           C  
HETATM   13  O4  UNL     1       3.756  -1.394   3.858  1.00  0.00           O  
HETATM   14  O5  UNL     1       2.506  -0.605   1.530  1.00  0.00           O  
HETATM   15  C9  UNL     1       2.687   0.332   0.512  1.00  0.00           C  
HETATM   16  O6  UNL     1       3.100  -0.330  -0.613  1.00  0.00           O  
HETATM   17  C10 UNL     1       4.347   0.119  -1.095  1.00  0.00           C  
HETATM   18  C11 UNL     1       4.147   0.650  -2.468  1.00  0.00           C  
HETATM   19  O7  UNL     1       3.646  -0.330  -3.335  1.00  0.00           O  
HETATM   20  C12 UNL     1       5.391   1.221  -3.095  1.00  0.00           C  
HETATM   21  O8  UNL     1       5.962   2.221  -2.311  1.00  0.00           O  
HETATM   22  C13 UNL     1       5.371  -1.017  -0.982  1.00  0.00           C  
HETATM   23  O9  UNL     1       6.618  -0.674  -1.410  1.00  0.00           O  
HETATM   24  C14 UNL     1       7.574  -0.531  -0.397  1.00  0.00           C  
HETATM   25  O10 UNL     1       7.849   0.846  -0.373  1.00  0.00           O  
HETATM   26  C15 UNL     1       9.040   1.218   0.152  1.00  0.00           C  
HETATM   27  C16 UNL     1       8.951   2.641   0.663  1.00  0.00           C  
HETATM   28  C17 UNL     1       9.612   0.285   1.195  1.00  0.00           C  
HETATM   29  O11 UNL     1       8.819   0.230   2.332  1.00  0.00           O  
HETATM   30  C18 UNL     1       9.805  -1.081   0.576  1.00  0.00           C  
HETATM   31  O12 UNL     1       9.553  -2.029   1.584  1.00  0.00           O  
HETATM   32  C19 UNL     1       8.835  -1.279  -0.595  1.00  0.00           C  
HETATM   33  O13 UNL     1       9.525  -0.802  -1.735  1.00  0.00           O  
HETATM   34  C20 UNL     1       4.849  -2.250  -1.654  1.00  0.00           C  
HETATM   35  O14 UNL     1       3.546  -2.481  -1.149  1.00  0.00           O  
HETATM   36  C21 UNL     1       5.649  -3.478  -1.398  1.00  0.00           C  
HETATM   37  O15 UNL     1       6.762  -3.684  -1.826  1.00  0.00           O  
HETATM   38  C22 UNL     1       1.430   1.110   0.304  1.00  0.00           C  
HETATM   39  O16 UNL     1       1.699   2.466   0.135  1.00  0.00           O  
HETATM   40  O17 UNL     1      -2.393  -0.784   1.926  1.00  0.00           O  
HETATM   41  C23 UNL     1      -3.551  -0.004   2.104  1.00  0.00           C  
HETATM   42  C24 UNL     1      -4.497  -0.622   3.112  1.00  0.00           C  
HETATM   43  O18 UNL     1      -5.595   0.258   3.185  1.00  0.00           O  
HETATM   44  C25 UNL     1      -4.221   0.304   0.805  1.00  0.00           C  
HETATM   45  O19 UNL     1      -4.196   1.632   0.435  1.00  0.00           O  
HETATM   46  C26 UNL     1      -5.461   2.199   0.279  1.00  0.00           C  
HETATM   47  O20 UNL     1      -5.683   2.545  -1.048  1.00  0.00           O  
HETATM   48  C27 UNL     1      -6.632   3.518  -1.218  1.00  0.00           C  
HETATM   49  C28 UNL     1      -8.000   3.118  -0.710  1.00  0.00           C  
HETATM   50  C29 UNL     1      -6.208   4.872  -0.654  1.00  0.00           C  
HETATM   51  O21 UNL     1      -7.346   5.632  -0.418  1.00  0.00           O  
HETATM   52  C30 UNL     1      -5.380   4.681   0.593  1.00  0.00           C  
HETATM   53  O22 UNL     1      -5.699   5.680   1.495  1.00  0.00           O  
HETATM   54  C31 UNL     1      -5.629   3.331   1.228  1.00  0.00           C  
HETATM   55  O23 UNL     1      -4.705   3.199   2.262  1.00  0.00           O  
HETATM   56  C32 UNL     1      -3.689  -0.551  -0.334  1.00  0.00           C  
HETATM   57  O24 UNL     1      -4.227  -1.808  -0.214  1.00  0.00           O  
HETATM   58  C33 UNL     1      -5.121  -2.147  -1.242  1.00  0.00           C  
HETATM   59  O25 UNL     1      -6.398  -2.369  -0.817  1.00  0.00           O  
HETATM   60  C34 UNL     1      -6.715  -3.618  -0.375  1.00  0.00           C  
HETATM   61  C35 UNL     1      -6.378  -3.842   1.084  1.00  0.00           C  
HETATM   62  O26 UNL     1      -7.083  -2.934   1.899  1.00  0.00           O  
HETATM   63  C36 UNL     1      -6.219  -4.753  -1.240  1.00  0.00           C  
HETATM   64  O27 UNL     1      -6.507  -5.951  -0.587  1.00  0.00           O  
HETATM   65  C37 UNL     1      -4.732  -4.608  -1.493  1.00  0.00           C  
HETATM   66  O28 UNL     1      -3.993  -4.724  -0.331  1.00  0.00           O  
HETATM   67  C38 UNL     1      -4.532  -3.242  -2.098  1.00  0.00           C  
HETATM   68  O29 UNL     1      -5.109  -3.153  -3.362  1.00  0.00           O  
HETATM   69  H1  UNL     1      -1.607   2.390  -3.129  1.00  0.00           H  
HETATM   70  H2  UNL     1       0.126   1.961  -3.247  1.00  0.00           H  
HETATM   71  H3  UNL     1      -1.047   1.345  -4.490  1.00  0.00           H  
HETATM   72  H4  UNL     1      -2.173   1.516  -0.985  1.00  0.00           H  
HETATM   73  H5  UNL     1      -1.764  -1.458  -0.824  1.00  0.00           H  
HETATM   74  H6  UNL     1      -1.848   0.957   1.056  1.00  0.00           H  
HETATM   75  H7  UNL     1      -0.398   1.653   1.317  1.00  0.00           H  
HETATM   76  H8  UNL     1       1.160   1.875   3.113  1.00  0.00           H  
HETATM   77  H9  UNL     1       0.002  -0.785   3.230  1.00  0.00           H  
HETATM   78  H10 UNL     1       3.140   0.864   2.820  1.00  0.00           H  
HETATM   79  H11 UNL     1       1.709  -1.673   3.818  1.00  0.00           H  
HETATM   80  H12 UNL     1       2.367  -0.271   4.838  1.00  0.00           H  
HETATM   81  H13 UNL     1       4.414  -0.734   3.548  1.00  0.00           H  
HETATM   82  H14 UNL     1       3.484   1.076   0.800  1.00  0.00           H  
HETATM   83  H15 UNL     1       4.638   0.952  -0.404  1.00  0.00           H  
HETATM   84  H16 UNL     1       3.346   1.466  -2.466  1.00  0.00           H  
HETATM   85  H17 UNL     1       3.712  -0.024  -4.280  1.00  0.00           H  
HETATM   86  H18 UNL     1       6.161   0.468  -3.339  1.00  0.00           H  
HETATM   87  H19 UNL     1       5.069   1.743  -4.042  1.00  0.00           H  
HETATM   88  H20 UNL     1       5.233   2.798  -1.915  1.00  0.00           H  
HETATM   89  H21 UNL     1       5.362  -1.218   0.138  1.00  0.00           H  
HETATM   90  H22 UNL     1       7.109  -0.767   0.585  1.00  0.00           H  
HETATM   91  H23 UNL     1       9.798   1.260  -0.683  1.00  0.00           H  
HETATM   92  H24 UNL     1       8.070   2.818   1.304  1.00  0.00           H  
HETATM   93  H25 UNL     1       8.932   3.294  -0.259  1.00  0.00           H  
HETATM   94  H26 UNL     1       9.901   2.918   1.170  1.00  0.00           H  
HETATM   95  H27 UNL     1      10.605   0.659   1.508  1.00  0.00           H  
HETATM   96  H28 UNL     1       9.358   0.258   3.176  1.00  0.00           H  
HETATM   97  H29 UNL     1      10.847  -1.179   0.248  1.00  0.00           H  
HETATM   98  H30 UNL     1      10.295  -2.094   2.216  1.00  0.00           H  
HETATM   99  H31 UNL     1       8.722  -2.378  -0.663  1.00  0.00           H  
HETATM  100  H32 UNL     1      10.120  -1.552  -2.008  1.00  0.00           H  
HETATM  101  H33 UNL     1       4.747  -2.167  -2.745  1.00  0.00           H  
HETATM  102  H34 UNL     1       2.996  -2.943  -1.848  1.00  0.00           H  
HETATM  103  H35 UNL     1       5.222  -4.258  -0.785  1.00  0.00           H  
HETATM  104  H36 UNL     1       0.978   0.782  -0.677  1.00  0.00           H  
HETATM  105  H37 UNL     1       0.958   2.947  -0.325  1.00  0.00           H  
HETATM  106  H38 UNL     1      -3.185   0.944   2.571  1.00  0.00           H  
HETATM  107  H39 UNL     1      -3.999  -0.631   4.098  1.00  0.00           H  
HETATM  108  H40 UNL     1      -4.848  -1.607   2.787  1.00  0.00           H  
HETATM  109  H41 UNL     1      -5.915   0.310   4.136  1.00  0.00           H  
HETATM  110  H42 UNL     1      -5.312   0.019   0.888  1.00  0.00           H  
HETATM  111  H43 UNL     1      -6.236   1.409   0.506  1.00  0.00           H  
HETATM  112  H44 UNL     1      -6.744   3.672  -2.317  1.00  0.00           H  
HETATM  113  H45 UNL     1      -8.351   3.909   0.017  1.00  0.00           H  
HETATM  114  H46 UNL     1      -8.014   2.112  -0.255  1.00  0.00           H  
HETATM  115  H47 UNL     1      -8.773   3.117  -1.509  1.00  0.00           H  
HETATM  116  H48 UNL     1      -5.534   5.334  -1.403  1.00  0.00           H  
HETATM  117  H49 UNL     1      -7.216   6.534  -0.839  1.00  0.00           H  
HETATM  118  H50 UNL     1      -4.284   4.722   0.379  1.00  0.00           H  
HETATM  119  H51 UNL     1      -5.951   6.526   1.035  1.00  0.00           H  
HETATM  120  H52 UNL     1      -6.639   3.269   1.716  1.00  0.00           H  
HETATM  121  H53 UNL     1      -4.832   3.928   2.918  1.00  0.00           H  
HETATM  122  H54 UNL     1      -4.122  -0.104  -1.260  1.00  0.00           H  
HETATM  123  H55 UNL     1      -5.155  -1.242  -1.922  1.00  0.00           H  
HETATM  124  H56 UNL     1      -7.843  -3.695  -0.419  1.00  0.00           H  
HETATM  125  H57 UNL     1      -6.676  -4.852   1.428  1.00  0.00           H  
HETATM  126  H58 UNL     1      -5.315  -3.709   1.314  1.00  0.00           H  
HETATM  127  H59 UNL     1      -6.838  -3.051   2.849  1.00  0.00           H  
HETATM  128  H60 UNL     1      -6.729  -4.651  -2.216  1.00  0.00           H  
HETATM  129  H61 UNL     1      -7.424  -5.825  -0.197  1.00  0.00           H  
HETATM  130  H62 UNL     1      -4.415  -5.378  -2.199  1.00  0.00           H  
HETATM  131  H63 UNL     1      -3.328  -5.433  -0.397  1.00  0.00           H  
HETATM  132  H64 UNL     1      -3.431  -3.076  -2.153  1.00  0.00           H  
HETATM  133  H65 UNL     1      -5.198  -4.085  -3.699  1.00  0.00           H  
CONECT    1    2   69   70   71
CONECT    2    3    3    4
CONECT    4    5   72
CONECT    5    6   56   73
CONECT    6    7   40   74
CONECT    7    8
CONECT    8    9   38   75
CONECT    9   10   11   76
CONECT   10   77
CONECT   11   12   14   78
CONECT   12   13   79   80
CONECT   13   81
CONECT   14   15
CONECT   15   16   38   82
CONECT   16   17
CONECT   17   18   22   83
CONECT   18   19   20   84
CONECT   19   85
CONECT   20   21   86   87
CONECT   21   88
CONECT   22   23   34   89
CONECT   23   24
CONECT   24   25   32   90
CONECT   25   26
CONECT   26   27   28   91
CONECT   27   92   93   94
CONECT   28   29   30   95
CONECT   29   96
CONECT   30   31   32   97
CONECT   31   98
CONECT   32   33   99
CONECT   33  100
CONECT   34   35   36  101
CONECT   35  102
CONECT   36   37   37  103
CONECT   38   39  104
CONECT   39  105
CONECT   40   41
CONECT   41   42   44  106
CONECT   42   43  107  108
CONECT   43  109
CONECT   44   45   56  110
CONECT   45   46
CONECT   46   47   54  111
CONECT   47   48
CONECT   48   49   50  112
CONECT   49  113  114  115
CONECT   50   51   52  116
CONECT   51  117
CONECT   52   53   54  118
CONECT   53  119
CONECT   54   55  120
CONECT   55  121
CONECT   56   57  122
CONECT   57   58
CONECT   58   59   67  123
CONECT   59   60
CONECT   60   61   63  124
CONECT   61   62  125  126
CONECT   62  127
CONECT   63   64   65  128
CONECT   64  129
CONECT   65   66   67  130
CONECT   66  131
CONECT   67   68  132
CONECT   68  133
END
Download

SMILES for HMDB0001986 (Lacto-N-difucopentaose II)

[H][C@@](O[C@@H]1O[C@H](CO)[C@H](O)[C@]([H])(O[C@@H]2O[C@H](CO)[C@@H](O[C@]3([H])O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]3O)[C@H](O[C@]3([H])O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)[C@H]2NC(C)=O)[C@H]1O)([C@H](O)CO)[C@]([H])(O[C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O)[C@H](O)C=O
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INCHI for HMDB0001986 (Lacto-N-difucopentaose II)

InChI=1S/C38H65NO29/c1-9-18(48)22(52)25(55)35(59-9)64-29(12(46)4-40)30(13(47)5-41)65-38-28(58)33(21(51)15(7-43)62-38)68-34-17(39-11(3)45)32(67-37-27(57)24(54)20(50)14(6-42)61-37)31(16(8-44)63-34)66-36-26(56)23(53)19(49)10(2)60-36/h4,9-10,12-38,41-44,46-58H,5-8H2,1-3H3,(H,39,45)/t9-,10-,12+,13+,14+,15+,16+,17+,18+,19+,20-,21-,22+,23+,24-,25-,26-,27+,28+,29+,30+,31+,32+,33-,34-,35-,36-,37-,38-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
lacto-N-Difucohexaose IIHMDB
LNDFH IIHMDB
O-6-Deoxy-a-L-galactopyranosyl-(1->3)-O-[O-6-deoxy-a-L-galactopyranosyl-(1->4)-O-[b-D-galactopyranosyl-(1->3)]-O-2-(acetylamino)-2-deoxy-b-D-glucopyranosyl-(1->3)-b-D-galactopyranosyl-(1->4)]- D-glucoseHMDB
O-6-Deoxy-alpha-L-galactopyranosyl-(1->3)-O-[O-6-deoxy-alpha-L-galactopyranosyl-(1->4)-O-[b-D-galactopyranosyl-(1->3)]-O-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->4)]- D-glucoseHMDB
O-6-Deoxy-alpha-L-galactopyranosyl-(1->3)-O-[O-6-deoxy-alpha-L-galactopyranosyl-(1->4)-O-[b-delta-galactopyranosyl-(1->3)]-O-2-(acetylamino)-2-deoxy-beta-delta-glucopyranosyl-(1->3)-beta-delta-galactopyranosyl-(1->4)]- D-glucoseHMDB
O-a-L-Fucopyranosyl-(1->4)-O-[b-D-galactopyranosyl-(1->3)]-O-2-acetamido-2-deoxy-b-D-glucopyranosyl-(1->3)-O-b-D-galactopyranosyl-(1->4)-O-[a-L-fucopyranosyl-(1->3)]- D-glucoseHMDB
O-alpha-L-Fucopyranosyl-(1->4)-O-[b-D-galactopyranosyl-(1->3)]-O-2-acetamido-2-deoxy-beta-D-glucopyranosyl-(1->3)-O-beta-D-galactopyranosyl-(1->4)-O-[a-L-fucopyranosyl-(1->3)]- D-glucoseHMDB
O-alpha-L-Fucopyranosyl-(1->4)-O-[b-delta-galactopyranosyl-(1->3)]-O-2-acetamido-2-deoxy-beta-delta-glucopyranosyl-(1->3)-O-beta-delta-galactopyranosyl-(1->4)-O-[a-L-fucopyranosyl-(1->3)]- D-glucoseHMDB
N-[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(2R,3R,4R,5S)-1,2,5-trihydroxy-6-oxo-4-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]ethanimidateGenerator, HMDB
Chemical FormulaC38H65NO29
Average Molecular Weight999.912
Monoisotopic Molecular Weight999.364225123
IUPAC NameN-[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(2R,3R,4R,5S)-1,2,5-trihydroxy-6-oxo-4-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]acetamide
Traditional NameN-[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-{[(2R,3R,4R,5S)-1,2,5-trihydroxy-6-oxo-4-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}hexan-3-yl]oxy}oxan-4-yl]oxy}-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-5-{[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl]acetamide
CAS Registry Number62258-12-2
SMILES
[H][C@@](O[C@@H]1O[C@H](CO)[C@H](O)[C@]([H])(O[C@@H]2O[C@H](CO)[C@@H](O[C@]3([H])O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]3O)[C@H](O[C@]3([H])O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)[C@H]2NC(C)=O)[C@H]1O)([C@H](O)CO)[C@]([H])(O[C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O)[C@H](O)C=O
InChI Identifier
InChI=1S/C38H65NO29/c1-9-18(48)22(52)25(55)35(59-9)64-29(12(46)4-40)30(13(47)5-41)65-38-28(58)33(21(51)15(7-43)62-38)68-34-17(39-11(3)45)32(67-37-27(57)24(54)20(50)14(6-42)61-37)31(16(8-44)63-34)66-36-26(56)23(53)19(49)10(2)60-36/h4,9-10,12-38,41-44,46-58H,5-8H2,1-3H3,(H,39,45)/t9-,10-,12+,13+,14+,15+,16+,17+,18+,19+,20-,21-,22+,23+,24-,25-,26-,27+,28+,29+,30+,31+,32+,33-,34-,35-,36-,37-,38-/m0/s1
InChI KeyQNSWVQWPVUZACH-ZQTNVGDNSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentOligosaccharides
Alternative Parents
Substituents
  • Oligosaccharide
  • Fatty acyl glycoside
  • N-acyl-alpha-hexosamine
  • Alkyl glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Oxane
  • Fatty acyl
  • Alpha-hydroxyaldehyde
  • Acetamide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Organoheterocyclic compound
  • Polyol
  • Acetal
  • Oxacycle
  • Carboxylic acid derivative
  • Alcohol
  • Organic oxide
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Aldehyde
  • Primary alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility128 g/LALOGPS
logP-2ALOGPS
logP-11ChemAxon
logS-0.89ALOGPS
pKa (Strongest Acidic)11.34ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count29ChemAxon
Hydrogen Donor Count18ChemAxon
Polar Surface Area482.38 ŲChemAxon
Rotatable Bond Count19ChemAxon
Refractivity207.43 m³·mol⁻¹ChemAxon
Polarizability93.61 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+280.732859911
AllCCS[M+H-H2O]+281.532859911
AllCCS[M+NH4]+280.032859911
AllCCS[M+Na]+279.832859911
AllCCS[M-H]-319.032859911
AllCCS[M+Na-2H]-324.032859911
AllCCS[M+HCOO]-329.532859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 10V, Positive-QTOFsplash10-0080-0103002094-987d215b0546aecf1b902017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 20V, Positive-QTOFsplash10-0573-0506105292-c4c353adb70f057166e52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 40V, Positive-QTOFsplash10-004u-2804019364-7bd6334e0a7f9c72b8212017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 10V, Negative-QTOFsplash10-001i-3111010149-36bb61502c0ba138818b2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 20V, Negative-QTOFsplash10-001i-3303223359-4a61a2f9dff985e0aa4e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 40V, Negative-QTOFsplash10-03mi-6947551010-ff04384c76802dcb152e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 10V, Positive-QTOFsplash10-0pe9-3309004042-7c114b64db76e1939d0b2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 20V, Positive-QTOFsplash10-0f7n-3902075432-7d020f22289150855b0c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 40V, Positive-QTOFsplash10-0002-4901011010-353aff4549c3a20c0fca2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 10V, Negative-QTOFsplash10-0002-1000000029-fce0808c0342fbc045d22021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 20V, Negative-QTOFsplash10-052e-2400001009-ac04f25d564d866f70cf2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lacto-N-difucopentaose II 40V, Negative-QTOFsplash10-08i9-6900004003-e9e52e2e8da3ac9d63522021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Breast Milk
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Breast MilkDetected and Quantified0.11 uMAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022783
KNApSAcK IDNot Available
Chemspider ID30776550
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53477740
PDB IDNot Available
ChEBI ID89338
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Engfer MB, Stahl B, Finke B, Sawatzki G, Daniel H: Human milk oligosaccharides are resistant to enzymatic hydrolysis in the upper gastrointestinal tract. Am J Clin Nutr. 2000 Jun;71(6):1589-96. [PubMed:10837303 ]
  2. Donald AS, Feeney J: Separation of human milk oligosaccharides by recycling chromatography. First isolation of lacto-N-neo-difucohexaose II and 3'-Galactosyllactose from this source. Carbohydr Res. 1988 Jul 15;178:79-91. [PubMed:3274083 ]
  3. Ninonuevo MR, Park Y, Yin H, Zhang J, Ward RE, Clowers BH, German JB, Freeman SL, Killeen K, Grimm R, Lebrilla CB: A strategy for annotating the human milk glycome. J Agric Food Chem. 2006 Oct 4;54(20):7471-80. [PubMed:17002410 ]
  4. Coppa GV, Pierani P, Zampini L, Bruni S, Carloni I, Gabrielli O: Characterization of oligosaccharides in milk and feces of breast-fed infants by high-performance anion-exchange chromatography. Adv Exp Med Biol. 2001;501:307-14. [PubMed:11787695 ]
  5. Von Seggern CE, Cotter RJ: Fragmentation studies of noncovalent sugar-sugar complexes by infrared atmospheric pressure MALDI. J Am Soc Mass Spectrom. 2003 Oct;14(10):1158-65. [PubMed:14530096 ]