NP-MRD: Showing NP-Card for Calditol (NP0022308)

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Record Information

Version

2.0

Created at

2021-01-06 07:30:58 UTC

Updated at

2021-07-15 17:38:41 UTC

NP-MRD ID

NP0022308

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Calditol

Provided By

NPAtlas

Description

Calditol is found in Sulfolobus sp. Calditol was first documented in 1995 (PMID: 7609602). Based on a literature review very few articles have been published on 5-(2,3-dihydroxypropoxy)-1-(hydroxymethyl)cyclopentane-1,2,3,4-tetrol (PMID: 18339312) (PMID: 30518563) (PMID: 28214513).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI

  Mrv1652306242105223D          

 35 35  0  0  0  0            999 V2000
    4.4283   -1.4182   -0.7776 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8984   -0.1636   -1.0641 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7277    0.1625   -0.1237 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2733    1.4029   -0.4752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7512   -0.9453   -0.2276 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6300   -0.8811    0.5001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2398    0.1227    0.3497 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6815    0.8287    1.6033 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6904    0.0306    2.7166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0897    1.3091    1.3201 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0142    0.7363    2.1948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.7807   -0.0690 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7686    0.3961   -0.1481 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5738   -0.4739   -0.1160 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0432   -1.4161    0.7639 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4507   -1.0024   -1.5280 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9786   -0.0274   -2.3703 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4979   -1.5952    0.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6381    0.6416   -1.0670 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4572   -0.2335   -2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1776    0.1350    0.9020 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0706    1.9497   -0.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4625   -1.0355   -1.3180 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2879   -1.8987   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0049    0.8995   -0.3967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0777    1.7393    1.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2638   -0.8427    2.6200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1987    2.3938    1.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5839    0.2855    2.9627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1339    1.4788   -0.8550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3044    1.2160   -0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8156   -1.8554    0.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4367   -1.3722   -1.8362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7775   -1.8806   -1.4795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7340    0.5330   -2.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
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  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
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 12 13  1  0  0  0  0
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 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 14  7  1  0  0  0  0
  1 18  1  0  0  0  0
  2 19  1  0  0  0  0
  2 20  1  0  0  0  0
  3 21  1  1  0  0  0
  4 22  1  0  0  0  0
  5 23  1  0  0  0  0
  5 24  1  0  0  0  0
  7 25  1  6  0  0  0
  8 26  1  1  0  0  0
  9 27  1  0  0  0  0
 10 28  1  6  0  0  0
 11 29  1  0  0  0  0
 12 30  1  6  0  0  0
 13 31  1  0  0  0  0
 15 32  1  0  0  0  0
 16 33  1  0  0  0  0
 16 34  1  0  0  0  0
 17 35  1  0  0  0  0
M  END

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
    4.4283   -1.4182   -0.7776 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8984   -0.1636   -1.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7277    0.1625   -0.1237 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2733    1.4029   -0.4752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7512   -0.9453   -0.2276 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6300   -0.8811    0.5001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2398    0.1227    0.3497 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6815    0.8287    1.6033 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6904    0.0306    2.7166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0897    1.3091    1.3201 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0142    0.7363    2.1948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.7807   -0.0690 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7686    0.3961   -0.1481 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5738   -0.4739   -0.1160 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0432   -1.4161    0.7639 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4507   -1.0024   -1.5280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9786   -0.0274   -2.3703 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4979   -1.5952    0.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6381    0.6416   -1.0670 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4572   -0.2335   -2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1776    0.1350    0.9020 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0706    1.9497   -0.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4625   -1.0355   -1.3180 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2879   -1.8987   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0049    0.8995   -0.3967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0777    1.7393    1.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2638   -0.8427    2.6200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1987    2.3938    1.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5839    0.2855    2.9627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1339    1.4788   -0.8550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3044    1.2160   -0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8156   -1.8554    0.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4367   -1.3722   -1.8362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7775   -1.8806   -1.4795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7340    0.5330   -2.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
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 14 16  1  0
 16 17  1  0
 14  7  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  1
  4 22  1  0
  5 23  1  0
  5 24  1  0
  7 25  1  6
  8 26  1  1
  9 27  1  0
 10 28  1  6
 11 29  1  0
 12 30  1  6
 13 31  1  0
 15 32  1  0
 16 33  1  0
 16 34  1  0
 17 35  1  0
M  END

  Mrv1652306242105223D          

 35 35  0  0  0  0            999 V2000
    4.4283   -1.4182   -0.7776 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8984   -0.1636   -1.0641 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7277    0.1625   -0.1237 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2733    1.4029   -0.4752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7512   -0.9453   -0.2276 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6300   -0.8811    0.5001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2398    0.1227    0.3497 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6815    0.8287    1.6033 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6904    0.0306    2.7166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0897    1.3091    1.3201 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0142    0.7363    2.1948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.7807   -0.0690 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7686    0.3961   -0.1481 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5738   -0.4739   -0.1160 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0432   -1.4161    0.7639 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4507   -1.0024   -1.5280 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9786   -0.0274   -2.3703 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4979   -1.5952    0.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6381    0.6416   -1.0670 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4572   -0.2335   -2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1776    0.1350    0.9020 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0706    1.9497   -0.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4625   -1.0355   -1.3180 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2879   -1.8987   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0049    0.8995   -0.3967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0777    1.7393    1.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2638   -0.8427    2.6200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1987    2.3938    1.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5839    0.2855    2.9627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1339    1.4788   -0.8550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3044    1.2160   -0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8156   -1.8554    0.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4367   -1.3722   -1.8362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7775   -1.8806   -1.4795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7340    0.5330   -2.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
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 14  7  1  0  0  0  0
  1 18  1  0  0  0  0
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  3 21  1  1  0  0  0
  4 22  1  0  0  0  0
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 10 28  1  6  0  0  0
 11 29  1  0  0  0  0
 12 30  1  6  0  0  0
 13 31  1  0  0  0  0
 15 32  1  0  0  0  0
 16 33  1  0  0  0  0
 16 34  1  0  0  0  0
 17 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0022308

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]([H])(O[H])C([H])([H])O[C@]1([H])[C@]([H])(O[H])[C@]([H])(O[H])[C@]([H])(O[H])[C@@]1(O[H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C9H18O8/c10-1-4(12)2-17-8-6(14)5(13)7(15)9(8,16)3-11/h4-8,10-16H,1-3H2/t4-,5+,6-,7+,8-,9+/m1/s1

> <INCHI_KEY>
JOKFCZVUUMLXSM-UHFFFAOYSA-N

> <FORMULA>
C9H18O8

> <MOLECULAR_WEIGHT>
254.235

> <EXACT_MASS>
254.10016754

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
23.131746938333585

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,3S,4R,5R)-5-[(2R)-2,3-dihydroxypropoxy]-1-(hydroxymethyl)cyclopentane-1,2,3,4-tetrol

> <ALOGPS_LOGP>
-2.66

> <JCHEM_LOGP>
-4.595318458666666

> <ALOGPS_LOGS>
0.33

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.806678482309746

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.879555087436993

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9682042763364747

> <JCHEM_POLAR_SURFACE_AREA>
150.84

> <JCHEM_REFRACTIVITY>
53.00039999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.47e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,3S,4R,5R)-5-[(2R)-2,3-dihydroxypropoxy]-1-(hydroxymethyl)cyclopentane-1,2,3,4-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
    4.4283   -1.4182   -0.7776 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8984   -0.1636   -1.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7277    0.1625   -0.1237 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2733    1.4029   -0.4752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7512   -0.9453   -0.2276 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6300   -0.8811    0.5001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2398    0.1227    0.3497 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6815    0.8287    1.6033 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6904    0.0306    2.7166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0897    1.3091    1.3201 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0142    0.7363    2.1948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.7807   -0.0690 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7686    0.3961   -0.1481 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5738   -0.4739   -0.1160 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0432   -1.4161    0.7639 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4507   -1.0024   -1.5280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9786   -0.0274   -2.3703 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4979   -1.5952    0.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6381    0.6416   -1.0670 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4572   -0.2335   -2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1776    0.1350    0.9020 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0706    1.9497   -0.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4625   -1.0355   -1.3180 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2879   -1.8987   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0049    0.8995   -0.3967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0777    1.7393    1.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2638   -0.8427    2.6200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1987    2.3938    1.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5839    0.2855    2.9627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1339    1.4788   -0.8550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3044    1.2160   -0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8156   -1.8554    0.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4367   -1.3722   -1.8362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7775   -1.8806   -1.4795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7340    0.5330   -2.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  1
 14 16  1  0
 16 17  1  0
 14  7  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  1
  4 22  1  0
  5 23  1  0
  5 24  1  0
  7 25  1  6
  8 26  1  1
  9 27  1  0
 10 28  1  6
 11 29  1  0
 12 30  1  6
 13 31  1  0
 15 32  1  0
 16 33  1  0
 16 34  1  0
 17 35  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0       4.428  -1.418  -0.778  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.898  -0.164  -1.064  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.728   0.163  -0.124  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.273   1.403  -0.475  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.751  -0.945  -0.228  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.630  -0.881   0.500  0.00  0.00           O+0
HETATM    7  C   UNK     0      -0.240   0.123   0.350  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.682   0.829   1.603  0.00  0.00           C+0
HETATM    9  O   UNK     0      -0.690   0.031   2.717  0.00  0.00           O+0
HETATM   10  C   UNK     0      -2.090   1.309   1.320  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.014   0.736   2.195  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.439   0.781  -0.069  0.00  0.00           C+0
HETATM   13  O   UNK     0      -3.769   0.396  -0.148  0.00  0.00           O+0
HETATM   14  C   UNK     0      -1.574  -0.474  -0.116  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.043  -1.416   0.764  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.451  -1.002  -1.528  0.00  0.00           C+0
HETATM   17  O   UNK     0      -0.979  -0.027  -2.370  0.00  0.00           O+0
HETATM   18  H   UNK     0       4.498  -1.595   0.179  0.00  0.00           H+0
HETATM   19  H   UNK     0       4.638   0.642  -1.067  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.457  -0.234  -2.085  0.00  0.00           H+0
HETATM   21  H   UNK     0       3.178   0.135   0.902  0.00  0.00           H+0
HETATM   22  H   UNK     0       3.071   1.950  -0.746  0.00  0.00           H+0
HETATM   23  H   UNK     0       1.462  -1.036  -1.318  0.00  0.00           H+0
HETATM   24  H   UNK     0       2.288  -1.899  -0.012  0.00  0.00           H+0
HETATM   25  H   UNK     0      -0.005   0.900  -0.397  0.00  0.00           H+0
HETATM   26  H   UNK     0      -0.078   1.739   1.814  0.00  0.00           H+0
HETATM   27  H   UNK     0      -0.264  -0.843   2.620  0.00  0.00           H+0
HETATM   28  H   UNK     0      -2.199   2.394   1.348  0.00  0.00           H+0
HETATM   29  H   UNK     0      -2.584   0.286   2.963  0.00  0.00           H+0
HETATM   30  H   UNK     0      -2.134   1.479  -0.855  0.00  0.00           H+0
HETATM   31  H   UNK     0      -4.304   1.216  -0.283  0.00  0.00           H+0
HETATM   32  H   UNK     0      -2.816  -1.855   0.371  0.00  0.00           H+0
HETATM   33  H   UNK     0      -2.437  -1.372  -1.836  0.00  0.00           H+0
HETATM   34  H   UNK     0      -0.778  -1.881  -1.480  0.00  0.00           H+0
HETATM   35  H   UNK     0      -1.734   0.533  -2.667  0.00  0.00           H+0
CONECT    1    2   18                                                       
CONECT    2    1    3   19   20                                             
CONECT    3    2    4    5   21                                             
CONECT    4    3   22                                                       
CONECT    5    3    6   23   24                                             
CONECT    6    5    7                                                       
CONECT    7    6    8   14   25                                             
CONECT    8    7    9   10   26                                             
CONECT    9    8   27                                                       
CONECT   10    8   11   12   28                                             
CONECT   11   10   29                                                       
CONECT   12   10   13   14   30                                             
CONECT   13   12   31                                                       
CONECT   14   12   15   16    7                                             
CONECT   15   14   32                                                       
CONECT   16   14   17   33   34                                             
CONECT   17   16   35                                                       
CONECT   18    1                                                            
CONECT   19    2                                                            
CONECT   20    2                                                            
CONECT   21    3                                                            
CONECT   22    4                                                            
CONECT   23    5                                                            
CONECT   24    5                                                            
CONECT   25    7                                                            
CONECT   26    8                                                            
CONECT   27    9                                                            
CONECT   28   10                                                            
CONECT   29   11                                                            
CONECT   30   12                                                            
CONECT   31   13                                                            
CONECT   32   15                                                            
CONECT   33   16                                                            
CONECT   34   16                                                            
CONECT   35   17                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   70    0
END

RDKit          3D

35 35  0  0  0  0  0  0  0  0999 V2000
    4.4283   -1.4182   -0.7776 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8984   -0.1636   -1.0641 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7277    0.1625   -0.1237 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2733    1.4029   -0.4752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7512   -0.9453   -0.2276 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6300   -0.8811    0.5001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2398    0.1227    0.3497 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6815    0.8287    1.6033 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6904    0.0306    2.7166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0897    1.3091    1.3201 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0142    0.7363    2.1948 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4390    0.7807   -0.0690 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.7686    0.3961   -0.1481 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5738   -0.4739   -0.1160 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0432   -1.4161    0.7639 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4507   -1.0024   -1.5280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9786   -0.0274   -2.3703 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4979   -1.5952    0.1786 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6381    0.6416   -1.0670 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4572   -0.2335   -2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1776    0.1350    0.9020 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0706    1.9497   -0.7460 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4625   -1.0355   -1.3180 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2879   -1.8987   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0049    0.8995   -0.3967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0777    1.7393    1.8142 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2638   -0.8427    2.6200 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1987    2.3938    1.3481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5839    0.2855    2.9627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1339    1.4788   -0.8550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3044    1.2160   -0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8156   -1.8554    0.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4367   -1.3722   -1.8362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7775   -1.8806   -1.4795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7340    0.5330   -2.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  1
 14 16  1  0
 16 17  1  0
 14  7  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  1
  4 22  1  0
  5 23  1  0
  5 24  1  0
  7 25  1  6
  8 26  1  1
  9 27  1  0
 10 28  1  6
 11 29  1  0
 12 30  1  6
 13 31  1  0
 15 32  1  0
 16 33  1  0
 16 34  1  0
 17 35  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₉H₁₈O₈

Average Mass

254.2350 Da

Monoisotopic Mass

254.10017 Da

IUPAC Name

(1S,2S,3S,4R,5R)-5-[(2R)-2,3-dihydroxypropoxy]-1-(hydroxymethyl)cyclopentane-1,2,3,4-tetrol

Traditional Name

(1S,2S,3S,4R,5R)-5-[(2R)-2,3-dihydroxypropoxy]-1-(hydroxymethyl)cyclopentane-1,2,3,4-tetrol

CAS Registry Number

Not Available

SMILES

OCC(O)COC1C(O)C(O)C(O)C1(O)CO

InChI Identifier

InChI=1S/C9H18O8/c10-1-4(12)2-17-8-6(14)5(13)7(15)9(8,16)3-11/h4-8,10-16H,1-3H2

InChI Key

JOKFCZVUUMLXSM-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Sulfolobus sp.	NPAtlas	7609602

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.7	ALOGPS
logP	-4.6	ChemAxon
logS	0.33	ALOGPS
pKa (Strongest Acidic)	11.88	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	150.84 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	53 m³·mol⁻¹	ChemAxon
Polarizability	23.13 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA013219

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78444840

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101918438

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Bode ML, Buddoo SR, Minnaar SH, du Plessis CA: Extraction, isolation and NMR data of the tetraether lipid calditoglycerocaldarchaeol (GDNT) from Sulfolobus metallicus harvested from a bioleaching reactor. Chem Phys Lipids. 2008 Aug;154(2):94-104. doi: 10.1016/j.chemphyslip.2008.02.005. Epub 2008 Mar 11. [PubMed:18339312 ]
Sugai A, Sakuma R, Fukuda I, Kurosawa N, Itoh YH, Kon K, Ando S, Itoh T: The structure of the core polyol of the ether lipids from Sulfolobus acidocaldarius. Lipids. 1995 Apr;30(4):339-44. doi: 10.1007/BF02536042. [PubMed:7609602 ]
Zeng Z, Liu XL, Wei JH, Summons RE, Welander PV: Calditol-linked membrane lipids are required for acid tolerance in Sulfolobus acidocaldarius. Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):12932-12937. doi: 10.1073/pnas.1814048115. Epub 2018 Dec 5. [PubMed:30518563 ]
Huguet C, Fietz S, Rosell-Mele A, Daura X, Costenaro L: Molecular dynamics simulation study of the effect of glycerol dialkyl glycerol tetraether hydroxylation on membrane thermostability. Biochim Biophys Acta Biomembr. 2017 May;1859(5):966-974. doi: 10.1016/j.bbamem.2017.02.009. Epub 2017 Feb 16. [PubMed:28214513 ]

Showing NP-Card for Calditol (NP0022308)

MOL for NP0022308 (Calditol)

3D MOL for NP0022308 (Calditol)

3D SDF for NP0022308 (Calditol)

3D-SDF for NP0022308 (Calditol)

PDB for NP0022308 (Calditol)

3D PDB for NP0022308 (Calditol)

SMILES for NP0022308 (Calditol)

INCHI for NP0022308 (Calditol)

Structure for NP0022308 (Calditol)

3D Structure for NP0022308 (Calditol)