Natural Product: NPC214702

Natural Product IDNPC214702
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (-)-(R)-Mellein
IUPAC Name (3R)-8-hydroxy-3-methyl-3,4-dihydroisochromen-1-one
Synonyms (R)-Mellein
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL499303
PubChem CID 114679
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003411] 2-benzopyrans

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey KWILGNNWGSNMPA-ZCFIWIBFSA-N
Standard InCHI InChI=1S/C10H10O3/c1-6-5-7-3-2-4-8(11)9(7)10(12)13-6/h2-4,6,11H,5H2,1H3/t6-/m1/s1
SMILES C[C@@H]1Cc2cccc(c2C(=O)O1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   178.06 Volume:   180.228
?
Van der Waals volume.
Dense:   0.988 LogP:   1.825
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.731
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.553
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   12.0
TPSA:   46.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.612 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.692 Fsp3:   0.3
MCE-18:   36.385
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.154 Fluc inhibitor:   0.347
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.25
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.249
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.855 Promiscuous compounds:   0.453

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.78 MDCK Permeability:   -4.576
Pgp-inhibitor:   0.373 Pgp-substrate:   0.079
PAMPA:   0.315
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.009
20% Bioavailability (F20%):   0.034 30% Bioavailability (F30%):   0.159
50% Bioavailability (F50%):   0.554

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.462 MRP1:   0.77
Plasma Protein Binding (PPB):   90.224% Volume Distribution (VD):   -0.234
Fu: 9.489%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.961
OATP1B3 inhibitor:   0.964 BCRP inhibitor:   0.075
BSEP inhibitor:   0.816

ADMET: Metabolism

CYP1A2-inhibitor:   0.005 CYP1A2-substrate:   0.743
CYP2C19-inhibitor:   0.006 CYP2C19-substrate:   0.084
CYP2C9-inhibitor:   0.002 CYP2C9-substrate:   0.095
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.082
CYP3A4-inhibitor:   0.164 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.996
HLM stability:   0.957
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  3.4 Half-life (T1/2):  1.217

ADMET: Toxicity

hERG Blockers:  0.03 hERG Blockers (10um):  0.397
Human Hepatotoxicity (H-HT):  0.529 Drug-induced Liver Injury (DILI):  0.744
AMES Toxicity:  0.931 Rat Oral Acute Toxicity:  0.664
Maximum Recommended Daily Dose:  0.636 Skin Sensitization:  0.998
Carcinogencity:  0.763 Eye Corrosion:  0.63
Eye Irritation:  0.978 Respiratory Toxicity:  0.538
Drug-induced Neurotoxicity:  0.794 Ototoxicity:  0.16
Hematotoxicity:  0.215 Drug-induced Nephrotoxicity:  0.848
Genotoxicity:  0.968 RPMI-8226 Immunitoxicity:  0.09
A549 Cytotoxicity:  0.412 Hek293 Cytotoxicity:  0.218
BCF:   1.211
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   3.658
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.83
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.027
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)00169-2]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[10075773]
NPO33476 microsphaeropsis sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[10869191]
NPO33476 microsphaeropsis sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[12027766]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. fruit n.a. PMID[15128023]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. PMID[16933891]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[18068204]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18464091]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18558747]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[18636777]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota stem bark Pangradin village, Jasinga, West Java, Indonesia 2005-AUG PMID[19839614]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[20817450]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. pericarp n.a. PMID[24555285]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[24717154]
NPO40491 Fagraea fragrans Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[26905094]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29244495]
NPO284 Albizia procera Species Fabaceae Eukaryota Bark n.a. n.a. PMID[30520635]
NPO33476 microsphaeropsis sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[32243151]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36364129]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota fruit hulls Madras, Tamil Nadu, India 1993-MAR PMID[9213587]
NPO40084 Coniothyrium sp. Species Coniothyriaceae Eukaryota n.a. n.a. n.a. PMID[9917295]
NPO33476 microsphaeropsis sp. Species n.a. Eukaryota n.a. n.a. n.a. PMID[9917295]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25216 Senecio vellereus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16885 Phonus arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16865.1 Prunus serrulata var. spontanea Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40491 Fagraea fragrans Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4421 Penicillium cyclopium Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3255 Lampranthus sociorum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40084 Coniothyrium sp. Species Coniothyriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5981 Achlys triphylla Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3415 Perymenium mendezii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO284 Albizia procera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Petiole n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16865.1 Prunus serrulata var. spontanea Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4421 Penicillium cyclopium Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5981 Achlys triphylla Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO284 Albizia procera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4952 Pertusaria amara Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3415 Perymenium mendezii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7616 Melanargia galathea Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3263 Thea sasanqua n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7464 Uruparia lanosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16865.1 Prunus serrulata var. spontanea Varieties Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6844 Bulbophyllum protractum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3255 Lampranthus sociorum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25216 Senecio vellereus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2963 Diospyros glaucifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16885 Phonus arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4117 Nauclea rhynchophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15597 Calystegia pubescens Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29287 Alectoria ochroleuca Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO855 Elymnias thryallis Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15401 Theobroma cacao Species Malvaceae 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 Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference
NPO15401 Theobroma cacao Dried Or Powder n.a. 0.029333333 n.a. n.a. mg/100g Database [PHENOL EXPLORER]

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

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT261 Individual protein Monoamine oxidase A Homo sapiens IC50 = 6200.0 nM PMID[30975503]
NPT582 Individual protein Monoamine oxidase B Homo sapiens IC50 = 50000.0 nM PMID[30975503]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT960 Organism Medicago sativa Medicago sativa GI = 100.0 % DOI[10.1016/S0953-7562(09)80766-1]
NPT1231 Organism Microbotryum violaceum Microbotryum violaceum IZ = 8.0 mm DOI[10.1016/S0953-7562(09)80766-1]
NPT3130 Organism Lepidium sativum Lepidium sativum GI = 100.0 % DOI[10.1016/S0953-7562(09)80766-1]
NPT1234 Organism Chlorella fusca Chlorella fusca IZ = 14.0 mm DOI[10.1016/S0953-7562(09)80766-1]
NPT19 Organism Escherichia coli Escherichia coli IZ = 2.0 mm DOI[10.1016/S0953-7562(09)80766-1]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[26905094]
NPT19 Organism Escherichia coli Escherichia coli MIC > 128.0 ug.mL-1 PMID[26905094]
NPT1232 Organism Eurotium repens Eurotium repens IZ = 6.0 mm DOI[10.1016/S0953-7562(09)80766-1]
NPT1233 Organism Mycotypha microspora Mycotypha microspora IZ = 0.0 mm DOI[10.1016/S0953-7562(09)80766-1]
NPT1230 Organism Bacillus megaterium Bacillus megaterium IZ = 2.0 mm DOI[10.1016/S0953-7562(09)80766-1]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC214702 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC470831
1.0 High Similarity NPC599777
0.6667 Remote Similarity NPC27407
0.65 Remote Similarity NPC195964
0.6383 Remote Similarity NPC142027
0.6098 Remote Similarity NPC235115
0.6098 Remote Similarity NPC488349
0.5952 Remote Similarity NPC291454
0.5814 Remote Similarity NPC470842
0.5682 Remote Similarity NPC603067
0.5556 Remote Similarity NPC145442
0.549 Remote Similarity NPC609639
0.5455 Remote Similarity NPC197666
0.5455 Remote Similarity NPC126739
0.5385 Remote Similarity NPC43627
0.5106 Remote Similarity NPC301915
0.5106 Remote Similarity NPC261292

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC214702 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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