Structure

Physi-Chem Properties

Molecular Weight:  134.02
Volume:  116.419
LogP:  -1.688
LogD:  -1.459
LogS:  0.114
# Rotatable Bonds:  3
TPSA:  94.83
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.317
Synthetic Accessibility Score:  2.893
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.967
MDCK Permeability:  0.0074933660216629505
Pgp-inhibitor:  0.0
Pgp-substrate:  0.066
Human Intestinal Absorption (HIA):  0.969
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.642
Plasma Protein Binding (PPB):  16.82231903076172%
Volume Distribution (VD):  0.278
Pgp-substrate:  76.02873992919922%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.043
CYP2C19-inhibitor:  0.032
CYP2C19-substrate:  0.051
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.392
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.132
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.027

ADMET: Excretion

Clearance (CL):  3.028
Half-life (T1/2):  0.852

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.16
Drug-inuced Liver Injury (DILI):  0.413
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.009
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.264
Carcinogencity:  0.013
Eye Corrosion:  0.019
Eye Irritation:  0.985
Respiratory Toxicity:  0.394

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC19044

Natural Product ID:  NPC19044
Common Name*:   (2R)-2-Hydroxybutanedioic Acid
IUPAC Name:   (2R)-2-hydroxybutanedioic acid
Synonyms:   (R)-2-Hydroxysuccinic Acid
Standard InCHIKey:  BJEPYKJPYRNKOW-UWTATZPHSA-N
Standard InCHI:  InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1
SMILES:  C([C@H](C(=O)O)O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL225986
PubChem CID:   92824
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0001713] Beta hydroxy acids and derivatives

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. fruit n.a. DOI[10.1007/s00217-007-0799-1]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. flower n.a. DOI[10.1016/j.foodchem.2011.01.077]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[10543912]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. PMID[11339628]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[11374978]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[11520216]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. PMID[11754604]
NPO28679 Prunus mume Species Rosaceae Eukaryota flowers n.a. n.a. PMID[12193020]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. stem n.a. PMID[12575075]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. leaf n.a. PMID[12575075]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12932131]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. Brazilian n.a. PMID[15387656]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[15577255]
NPO21349 Punica granatum Species Lythraceae Eukaryota Seeds n.a. n.a. PMID[15620261]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15679317]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. ripe fruit n.a. PMID[16205005]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[16297615]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[16562834]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. branch n.a. PMID[17202693]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. bark n.a. PMID[17260795]
NPO4044 Homalomena occulta Species Araceae Eukaryota n.a. aerial part n.a. PMID[17511005]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[17997069]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[18341288]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. whole plant n.a. PMID[18543151]
NPO4044 Homalomena occulta Species Araceae Eukaryota n.a. rhizome n.a. PMID[18649899]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota Roots Simao city, Yunnan Province, China 2007-MAY PMID[19374435]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. Daejeon, Korea 2007-Jan PMID[19670875]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20460582]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. seed n.a. PMID[20822014]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. root n.a. PMID[22547314]
NPO4044 Homalomena occulta Species Araceae Eukaryota n.a. rhizome n.a. PMID[22573367]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[23265871]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. fruit n.a. PMID[24155209]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[24358188]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota root bark Bozhou, Anhui Province, China 2010-AUG PMID[24377852]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. flower n.a. PMID[24504864]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota Flowers LuoYang, HeNan, China n.a. PMID[24621197]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[24959987]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[25172746]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[25302569]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. PMID[27617953]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota Roots n.a. n.a. PMID[28257196]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota Fruits n.a. n.a. PMID[29140705]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30188125]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[32004936]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[32881525]
NPO18932 Melia azedarach Species Meliaceae Eukaryota Fruits n.a. n.a. PMID[33253570]
NPO18932 Melia azedarach Species Meliaceae Eukaryota Seeds n.a. n.a. PMID[3701342]
NPO28159 Rubia akane Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[8176404]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[8778246]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8910532]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO21349 Punica granatum Species Lythraceae Eukaryota Root Bark n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Stem Bark n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Twig n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Roots n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO21349 Punica granatum Species Lythraceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO78 Rhizoma homalomenae occultae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18932.1 Melia azedarach var. toosendan Varieties Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23448 Vinegar n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4044 Homalomena occulta Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16931 Cichorium glandulosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18932.1 Melia azedarach var. toosendan Varieties Meliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4044 Homalomena occulta Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2837 Aloe spicata Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28159 Rubia akane Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22550 Paeonia suffruticosa Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18932.1 Melia azedarach var. toosendan Varieties Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28159 Rubia akane Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4044 Homalomena occulta Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18932 Melia azedarach Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28450 Phyllanthus emblica Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7385 Schisandra sphenanthera Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO523 Tussilago farfara Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16931 Cichorium glandulosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1474 Individual Protein ATP-dependent Clp protease proteolytic subunit Bacillus subtilis (strain 168) Potency n.a. 3981.1 nM PMID[526235]
NPT160 Individual Protein TAR DNA-binding protein 43 Homo sapiens Potency n.a. 3981.1 nM PMID[526235]
NPT93 Individual Protein Survival motor neuron protein Homo sapiens Potency = 1258.9 nM PMID[526235]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 10417.9 nM PMID[526235]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC19044 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC100742
1.0 High Similarity NPC97444
1.0 High Similarity NPC192402
1.0 High Similarity NPC24751
1.0 High Similarity NPC121018
0.9487 High Similarity NPC35661
0.8205 Intermediate Similarity NPC159089
0.8043 Intermediate Similarity NPC328954
0.7907 Intermediate Similarity NPC313565
0.7907 Intermediate Similarity NPC259982
0.7907 Intermediate Similarity NPC228782
0.7755 Intermediate Similarity NPC19676
0.7755 Intermediate Similarity NPC323401
0.775 Intermediate Similarity NPC5505
0.775 Intermediate Similarity NPC1037
0.76 Intermediate Similarity NPC6883
0.7556 Intermediate Similarity NPC242655
0.7556 Intermediate Similarity NPC270088
0.7556 Intermediate Similarity NPC38891
0.7551 Intermediate Similarity NPC277878
0.75 Intermediate Similarity NPC191084
0.75 Intermediate Similarity NPC250870
0.75 Intermediate Similarity NPC168052
0.7442 Intermediate Similarity NPC320331
0.74 Intermediate Similarity NPC196612
0.7273 Intermediate Similarity NPC322956
0.7273 Intermediate Similarity NPC325307
0.7209 Intermediate Similarity NPC222792
0.7209 Intermediate Similarity NPC316217
0.7179 Intermediate Similarity NPC307739
0.7179 Intermediate Similarity NPC76217
0.717 Intermediate Similarity NPC327895
0.717 Intermediate Similarity NPC43169
0.717 Intermediate Similarity NPC112224
0.717 Intermediate Similarity NPC93861
0.7083 Intermediate Similarity NPC172086
0.7083 Intermediate Similarity NPC247546
0.6939 Remote Similarity NPC293378
0.6939 Remote Similarity NPC46254
0.6923 Remote Similarity NPC198126
0.6852 Remote Similarity NPC61567
0.6852 Remote Similarity NPC220922
0.6852 Remote Similarity NPC293692
0.6842 Remote Similarity NPC236709
0.675 Remote Similarity NPC261351
0.6731 Remote Similarity NPC65985
0.6667 Remote Similarity NPC198377
0.6667 Remote Similarity NPC325165
0.6607 Remote Similarity NPC323945
0.6596 Remote Similarity NPC320624
0.6596 Remote Similarity NPC318951
0.6596 Remote Similarity NPC319680
0.6512 Remote Similarity NPC103612
0.6512 Remote Similarity NPC24967
0.6491 Remote Similarity NPC320296
0.6481 Remote Similarity NPC68743
0.6481 Remote Similarity NPC60830
0.6429 Remote Similarity NPC179624
0.641 Remote Similarity NPC301586
0.641 Remote Similarity NPC33415
0.6364 Remote Similarity NPC317945
0.6279 Remote Similarity NPC316685
0.6271 Remote Similarity NPC317651
0.6271 Remote Similarity NPC258690
0.625 Remote Similarity NPC292641
0.6222 Remote Similarity NPC128713
0.6154 Remote Similarity NPC320326
0.6098 Remote Similarity NPC320981
0.6071 Remote Similarity NPC3547
0.6053 Remote Similarity NPC165122
0.6034 Remote Similarity NPC17935
0.5952 Remote Similarity NPC187058
0.5952 Remote Similarity NPC182541
0.5952 Remote Similarity NPC197207
0.5952 Remote Similarity NPC149070
0.5952 Remote Similarity NPC212144
0.5952 Remote Similarity NPC127074
0.5897 Remote Similarity NPC3343
0.5873 Remote Similarity NPC32148
0.587 Remote Similarity NPC328950
0.5854 Remote Similarity NPC180423
0.5854 Remote Similarity NPC270334
0.5814 Remote Similarity NPC217218
0.5814 Remote Similarity NPC108238
0.5769 Remote Similarity NPC327542
0.5769 Remote Similarity NPC131770
0.5769 Remote Similarity NPC200618
0.5738 Remote Similarity NPC268243
0.5714 Remote Similarity NPC241404
0.5682 Remote Similarity NPC127142
0.5682 Remote Similarity NPC7814
0.5682 Remote Similarity NPC307027
0.566 Remote Similarity NPC93888
0.566 Remote Similarity NPC270805
0.5652 Remote Similarity NPC321569
0.5641 Remote Similarity NPC82694

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC19044 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
1.0 High Similarity NPD8604 Approved
1.0 High Similarity NPD8605 Approved
1.0 High Similarity NPD8603 Approved
1.0 High Similarity NPD8602 Approved
1.0 High Similarity NPD8598 Approved
1.0 High Similarity NPD8600 Approved
1.0 High Similarity NPD8599 Approved
1.0 High Similarity NPD8601 Approved
0.7551 Intermediate Similarity NPD9010 Approved
0.7551 Intermediate Similarity NPD9008 Approved
0.7551 Intermediate Similarity NPD65 Approved
0.7551 Intermediate Similarity NPD8960 Approved
0.7551 Intermediate Similarity NPD9011 Approved
0.7551 Intermediate Similarity NPD9007 Approved
0.7551 Intermediate Similarity NPD9009 Approved
0.7551 Intermediate Similarity NPD64 Approved
0.7551 Intermediate Similarity NPD72 Approved
0.7551 Intermediate Similarity NPD66 Approved
0.7179 Intermediate Similarity NPD8205 Approved
0.7179 Intermediate Similarity NPD8202 Approved
0.7105 Intermediate Similarity NPD8619 Approved
0.7105 Intermediate Similarity NPD8617 Approved
0.7083 Intermediate Similarity NPD9005 Phase 3
0.7083 Intermediate Similarity NPD70 Approved
0.7083 Intermediate Similarity NPD9004 Approved
0.7083 Intermediate Similarity NPD9003 Clinical (unspecified phase)
0.7083 Intermediate Similarity NPD109 Approved
0.7083 Intermediate Similarity NPD9128 Approved
0.7083 Intermediate Similarity NPD9124 Approved
0.7083 Intermediate Similarity NPD9125 Approved
0.7083 Intermediate Similarity NPD9127 Approved
0.7083 Intermediate Similarity NPD9122 Approved
0.7083 Intermediate Similarity NPD9130 Phase 3
0.7083 Intermediate Similarity NPD9123 Approved
0.7083 Intermediate Similarity NPD108 Approved
0.7083 Intermediate Similarity NPD9121 Approved
0.6981 Remote Similarity NPD73 Approved
0.6939 Remote Similarity NPD71 Approved
0.6939 Remote Similarity NPD9126 Approved
0.6939 Remote Similarity NPD9129 Approved
0.6923 Remote Similarity NPD8618 Approved
0.6923 Remote Similarity NPD55 Approved
0.6923 Remote Similarity NPD8204 Approved
0.6923 Remote Similarity NPD8203 Approved
0.6923 Remote Similarity NPD54 Approved
0.6923 Remote Similarity NPD8206 Approved
0.6852 Remote Similarity NPD8959 Approved
0.6842 Remote Similarity NPD8593 Approved
0.6842 Remote Similarity NPD8594 Approved
0.6667 Remote Similarity NPD9002 Approved
0.6667 Remote Similarity NPD9001 Clinical (unspecified phase)
0.641 Remote Similarity NPD8549 Clinical (unspecified phase)
0.6275 Remote Similarity NPD8964 Approved
0.6271 Remote Similarity NPD8961 Approved
0.6098 Remote Similarity NPD8590 Approved
0.6053 Remote Similarity NPD8592 Approved
0.6053 Remote Similarity NPD8591 Approved
0.5952 Remote Similarity NPD8814 Phase 3
0.5932 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5909 Remote Similarity NPD8596 Approved
0.5873 Remote Similarity NPD897 Approved
0.5873 Remote Similarity NPD896 Approved
0.5873 Remote Similarity NPD898 Approved
0.5778 Remote Similarity NPD8597 Approved
0.5682 Remote Similarity NPD8857 Approved
0.5682 Remote Similarity NPD900 Approved
0.566 Remote Similarity NPD8624 Approved
0.5641 Remote Similarity NPD8207 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data