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Showing NP-Card for D-threo-Isocitric acid (NP0000486)

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Record Information
Version2.0
Created at2006-02-23 12:38:32 UTC
Updated at2021-06-29 00:47:15 UTC
NP-MRD IDNP0000486
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-threo-Isocitric acid
DescriptionD-threo-Isocitric acid, also known as isocitrate or isocitrIC ACID, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. D-threo-Isocitric acid exists in all living species, ranging from bacteria to humans. D-threo-Isocitric acid has been detected, but not quantified in several different foods, such as citrus, fruits, common beans, green beans, and yellow wax beans.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000486 (D-threo-Isocitric acid)


  Mrv1652309042000252D          

 13 12  0  0  1  0            999 V2000
    4.3862   -4.6980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1007   -4.2855    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8152   -4.6980    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5297   -4.2855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2441   -4.6980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5297   -3.4605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8152   -5.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1007   -3.4604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8152   -3.0480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3862   -3.0479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -4.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9572   -4.6980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -3.4604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  2  0  0  0  0
  3  7  1  6  0  0  0
  2  8  1  6  0  0  0
  9  8  1  0  0  0  0
 10  8  2  0  0  0  0
 11  1  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  2  0  0  0  0
M  END
Download

3D MOL for NP0000486 (D-threo-Isocitric acid)

HMDB0001874
     RDKit          3D
D-threo-Isocitric acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -0.1530   -2.4846    0.7083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8711   -1.8882   -0.1290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5097   -2.7156   -1.0680 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1178   -0.4589   -0.2410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2690    0.4495    0.5756 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8482    1.8366    0.2967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1265    2.7085   -0.2059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1602    2.1329    0.5949 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.6144    0.0589 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7366    1.4879    1.0307 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9757   -0.5604   -0.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8280   -0.8524    0.8189 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8438   -1.4099   -1.1338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4945   -2.6170   -1.2907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2128   -0.2929   -0.0202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796   -0.1634   -1.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3209    0.3206    1.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3531    2.4106    1.5656 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0783    1.1728   -0.9035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1864    2.2494    0.5793 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6087   -1.9399   -1.5250 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
 13 21  1  0
M  END
Download

3D SDF for NP0000486 (D-threo-Isocitric acid)


  Mrv1652309042000252D          

 13 12  0  0  1  0            999 V2000
    4.3862   -4.6980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1007   -4.2855    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.8152   -4.6980    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5297   -4.2855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2441   -4.6980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5297   -3.4605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8152   -5.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1007   -3.4604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8152   -3.0480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3862   -3.0479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -4.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9572   -4.6980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6718   -3.4604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  2  0  0  0  0
  3  7  1  6  0  0  0
  2  8  1  6  0  0  0
  9  8  1  0  0  0  0
 10  8  2  0  0  0  0
 11  1  1  0  0  0  0
 12 11  1  0  0  0  0
 13 11  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0000486

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]([C@H](CC(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O7/c7-3(8)1-2(5(10)11)4(9)6(12)13/h2,4,9H,1H2,(H,7,8)(H,10,11)(H,12,13)/t2-,4+/m0/s1

> <INCHI_KEY>
ODBLHEXUDAPZAU-ZAFYKAAXSA-N

> <FORMULA>
C6H8O7

> <MOLECULAR_WEIGHT>
192.1235

> <EXACT_MASS>
192.02700261

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
15.536697322949372

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S)-1-hydroxypropane-1,2,3-tricarboxylic acid

> <ALOGPS_LOGP>
-0.35

> <JCHEM_LOGP>
-1.4463282496666667

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
4.676758742531204

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.068323851495592

> <JCHEM_PKA_STRONGEST_BASIC>
-4.021353286822632

> <JCHEM_POLAR_SURFACE_AREA>
132.13000000000002

> <JCHEM_REFRACTIVITY>
35.716100000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.25e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
threo-DS(+)-isocitrate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000486 (D-threo-Isocitric acid)

HMDB0001874
     RDKit          3D
D-threo-Isocitric acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -0.1530   -2.4846    0.7083 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8711   -1.8882   -0.1290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5097   -2.7156   -1.0680 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1178   -0.4589   -0.2410 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2690    0.4495    0.5756 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8482    1.8366    0.2967 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1265    2.7085   -0.2059 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1602    2.1329    0.5949 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1589    0.6144    0.0589 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7366    1.4879    1.0307 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9757   -0.5604   -0.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8280   -0.8524    0.8189 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8438   -1.4099   -1.1338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4945   -2.6170   -1.2907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2128   -0.2929   -0.0202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796   -0.1634   -1.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3209    0.3206    1.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3531    2.4106    1.5656 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0783    1.1728   -0.9035 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1864    2.2494    0.5793 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6087   -1.9399   -1.5250 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  5  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 11 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  1
  8 18  1  0
  9 19  1  6
 10 20  1  0
 13 21  1  0
M  END
Download

PDB for NP0000486 (D-threo-Isocitric acid)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       8.188  -8.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.521  -8.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.855  -8.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.189  -8.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      13.522  -8.770   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      12.189  -6.460   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      10.855 -10.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.521  -6.459   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      10.855  -5.690   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.188  -5.689   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.854  -7.999   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.520  -8.770   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       6.854  -6.459   0.000  0.00  0.00           O+0
CONECT    1    2   11                                                       
CONECT    2    1    3    8                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3                                                            
CONECT    8    2    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    1   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for NP0000486 (D-threo-Isocitric acid)

COMPND    HMDB0001874
HETATM    1  O1  UNL     1      -0.153  -2.485   0.708  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.871  -1.888  -0.129  1.00  0.00           C  
HETATM    3  O2  UNL     1      -1.510  -2.716  -1.068  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.118  -0.459  -0.241  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.269   0.450   0.576  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.848   1.837   0.297  1.00  0.00           C  
HETATM    7  O3  UNL     1      -0.126   2.709  -0.206  1.00  0.00           O  
HETATM    8  O4  UNL     1      -2.160   2.133   0.595  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.159   0.614   0.059  1.00  0.00           C  
HETATM   10  O5  UNL     1       1.737   1.488   1.031  1.00  0.00           O  
HETATM   11  C6  UNL     1       1.976  -0.560  -0.048  1.00  0.00           C  
HETATM   12  O6  UNL     1       2.828  -0.852   0.819  1.00  0.00           O  
HETATM   13  O7  UNL     1       1.844  -1.410  -1.134  1.00  0.00           O  
HETATM   14  H1  UNL     1      -2.494  -2.617  -1.291  1.00  0.00           H  
HETATM   15  H2  UNL     1      -2.213  -0.293  -0.020  1.00  0.00           H  
HETATM   16  H3  UNL     1      -0.980  -0.163  -1.319  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.321   0.321   1.655  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.353   2.411   1.566  1.00  0.00           H  
HETATM   19  H6  UNL     1       1.078   1.173  -0.904  1.00  0.00           H  
HETATM   20  H7  UNL     1       2.186   2.249   0.579  1.00  0.00           H  
HETATM   21  H8  UNL     1       2.609  -1.940  -1.525  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6    9   17
CONECT    6    7    7    8
CONECT    8   18
CONECT    9   10   11   19
CONECT   10   20
CONECT   11   12   12   13
CONECT   13   21
END
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SMILES for NP0000486 (D-threo-Isocitric acid)

O[C@H]([C@H](CC(O)=O)C(O)=O)C(O)=O
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INCHI for NP0000486 (D-threo-Isocitric acid)

InChI=1S/C6H8O7/c7-3(8)1-2(5(10)11)4(9)6(12)13/h2,4,9H,1H2,(H,7,8)(H,10,11)(H,12,13)/t2-,4+/m0/s1
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View in JSmol
Synonyms
ValueSource
(+)-Threo-isocitric acidChEBI
ISOCITRIC ACIDChEBI
(+)-Threo-isocitrateGenerator
ISOCITRateGenerator
D-Threo-isocitrateGenerator
(1R,2S)-1-Hydroxypropane-1,2,3-tricarboxylateHMDB
(1R,2S)-1-Hydroxypropane-1,2,3-tricarboxylic acidHMDB
(2R,3S)-IsocitrateHMDB
3-Carboxy-2,3-dideoxy-L-threo-pentaric acidHMDB
D-(+)-Threo-isocitric acid(2R,3S)-isocitric acidHMDB
DS-Threo-isocitrateHMDB
DS-Threo-isocitric acidHMDB
ICIHMDB
ICTHMDB
Threo-D-(+)-isocitrateHMDB
Threo-D-(+)-isocitric acidHMDB
Threo-DS(+)-isocitrateHMDB
Threo-DS(+)-isocitric acidHMDB
Threo-isocitrateHMDB
Isocitric acid, trisodium saltHMDB
Isocitric acid, (11)C-labeledHMDB
Isocitric acid, disodium saltHMDB
Isocitric acid, calcium saltHMDB
Isocitric acid, potassium saltHMDB
Isocitric acid, sodium saltHMDB
Chemical FormulaC6H8O7
Average Mass192.1235 Da
Monoisotopic Mass192.02700 Da
IUPAC Name(1R,2S)-1-hydroxypropane-1,2,3-tricarboxylic acid
Traditional Namethreo-DS(+)-isocitrate
CAS Registry Number6061-97-8
SMILES
O[C@H]([C@H](CC(O)=O)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C6H8O7/c7-3(8)1-2(5(10)11)4(9)6(12)13/h2,4,9H,1H2,(H,7,8)(H,10,11)(H,12,13)/t2-,4+/m0/s1
InChI KeyODBLHEXUDAPZAU-ZAFYKAAXSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arabidopsis thalianaKNApSAcK Database
Bryophyllum calycinumKNApSAcK Database
Cannabis sativaCannabisDB
      Not Available
Citrus limonKNApSAcK Database
Panax ginsengKNApSAcK Database
Phaseolus vulgarisKNApSAcK Database
Rubus spp.KNApSAcK Database
Triticum aestivumKNApSAcK Database
Species Where Detected
Species NameSourceReference
Escherichia coliKNApSAcK Database
Homo sapiens (Urine)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTricarboxylic acids and derivatives
Direct ParentTricarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
  • Beta-hydroxy acid
  • Monosaccharide
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Secondary alcohol
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility52.5 g/LALOGPS
logP-0.35ALOGPS
logP-1.4ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)3.07ChemAxon
pKa (Strongest Basic)-4ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area132.13 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity35.72 m³·mol⁻¹ChemAxon
Polarizability15.54 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001874
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012771
KNApSAcK IDC00001188
Chemspider ID4477081
KEGG Compound IDC00451
BioCyc IDTHREO-DS-ISO-CITRATE
BiGG ID34579
Wikipedia LinkNot Available
METLIN ID3328
PubChem Compound5318532
PDB IDNot Available
ChEBI ID151
Good Scents IDNot Available
References
General References
  1. Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DC, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, O'Donoghue K, Hester SS, Dunkley TP, Hart SR, Swainston N, Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG: Growth control of the eukaryote cell: a systems biology study in yeast. J Biol. 2007;6(2):4. doi: 10.1186/jbiol54. [PubMed:17439666 ]
  2. Hsu WH, Wang SJ, Chao YM, Chen CJ, Wang YF, Fuh JL, Chen SP, Lin YL: Urine metabolomics signatures in reversible cerebral vasoconstriction syndrome. Cephalalgia. 2020 Jun;40(7):735-747. doi: 10.1177/0333102419897621. Epub 2020 Jan 7. [PubMed:31910660 ]