Natural Product: NPC1838

Natural Product IDNPC1838
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 RKQDKXOBRXTSFS-PIHCAMFYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5352470
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000159] Epoxides

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 RKQDKXOBRXTSFS-PIHCAMFYSA-N
Standard InCHI InChI=1S/C15H24O/c1-12-7-5-9-14(2,3)11-13-15(4,16-13)10-6-8-12/h5,8-9,13H,6-7,10-11H2,1-4H3/b9-5+,12-8+
SMILES C/C/1=CCCC2(C)C(CC(C)(C)/C=C/C1)O2

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   220.18 Volume:   254.401
?
Van der Waals volume.
Dense:   0.865 LogP:   4.21
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.544
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.323
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   13.0
TPSA:   12.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.439 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.564 Fsp3:   0.733
MCE-18:   35.538
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.312 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.051
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.992 Promiscuous compounds:   0.02

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.508 MDCK Permeability:   -4.761
Pgp-inhibitor:   1.0 Pgp-substrate:   0.0
PAMPA:   0.0
?
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):   0.069
20% Bioavailability (F20%):   0.362 30% Bioavailability (F30%):   0.712
50% Bioavailability (F50%):   0.831

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.646
Plasma Protein Binding (PPB):   96.807% Volume Distribution (VD):   0.298
Fu: 3.462%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.018
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.574 CYP1A2-substrate:   0.989
CYP2C19-inhibitor:   0.727 CYP2C19-substrate:   0.012
CYP2C9-inhibitor:   0.511 CYP2C9-substrate:   0.094
CYP2D6-inhibitor:   0.663 CYP2D6-substrate:   0.555
CYP3A4-inhibitor:   0.026 CYP3A4-substrate:   0.879
CYP2B6-substrate:   0.926 CYP2C8-inhibitor:   0.998
HLM stability:   0.847
?
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):  9.142 Half-life (T1/2):  0.413

ADMET: Toxicity

hERG Blockers:  0.099 hERG Blockers (10um):  0.269
Human Hepatotoxicity (H-HT):  0.589 Drug-induced Liver Injury (DILI):  0.277
AMES Toxicity:  0.307 Rat Oral Acute Toxicity:  0.222
Maximum Recommended Daily Dose:  0.51 Skin Sensitization:  0.867
Carcinogencity:  0.589 Eye Corrosion:  0.335
Eye Irritation:  0.965 Respiratory Toxicity:  0.659
Drug-induced Neurotoxicity:  0.694 Ototoxicity:  0.137
Hematotoxicity:  0.109 Drug-induced Nephrotoxicity:  0.279
Genotoxicity:  0.295 RPMI-8226 Immunitoxicity:  0.108
A549 Cytotoxicity:  0.092 Hek293 Cytotoxicity:  0.343
BCF:   2.957
?
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:   4.248
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.211
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.107
?
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
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11240-015-0798-z]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(81)85171-0]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. DOI[10.1016/0045-6535(91)90110-Y]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.abb.2017.09.009]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.fitote.2006.01.011]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.plaphy.2005.07.013]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0885-5765(05)80069-4]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. whole plant n.a. DOI[10.1016/S1572-557X(05)02007-6]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50031a011]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1078/0176-1617-00195]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1155/2014/609649]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[10336650]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[10757735]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[11514174]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota fruit Hainan Island, China 1998 PMID[12398545]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[14735439]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[15679315]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. callus n.a. PMID[15715262]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[16252923]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[17624889]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[18220354]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18303850]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18611049]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18681481]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18768384]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19344127]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19476340]
NPO30686 Citrus hystrix Species Rutaceae Eukaryota n.a. exocarp n.a. PMID[20964319]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. root n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. exocarp n.a. PMID[21800857]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. aerial part n.a. PMID[21902175]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[21912858]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[22111577]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. flower n.a. PMID[22166201]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[22277277]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[23583435]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[23790907]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[24948953]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[25564559]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[25757283]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[26000707]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[28445039]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[29154541]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota Roots n.a. n.a. PMID[30024167]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[30384263]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[32560389]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[32880179]
NPO2819 Angelica sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36085404]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[36336219]
NPO45619 Myrcia sylvatica Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[36558108]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[36558187]
NPO56319 Polygonum persicaria Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[36558187]
NPO30740 Polygonum lapathifolium Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[36558187]
NPO52082 Polygonum arenarium Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[36558187]
NPO59573 Polygonum bellardii Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[36558187]
NPO56945 Polygonum cognatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[36558187]
NPO59691 Myrtus communis subsp. tarentina Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[36986980]
NPO2819 Angelica sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37245156]
NPO14532 Salmea scandens Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37278000]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[37446590]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[37447270]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[37631012]
NPO30686 Citrus hystrix Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[38067483]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[38217369]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[38354824]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[38927152]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[39064881]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[39199155]
NPO57652 Cymbopogon flexousus Genus Poaceae Eukaryota n.a. n.a. n.a. PMID[39243337]
NPO46452 Eugenia luschnathiana Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[39292142]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30686 Citrus hystrix Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30740 Polygonum lapathifolium Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2761 Cynanchum stauntoni Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4460 Vincetoxicum glaucescens Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10366 Vincetoxicum stauntonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Roots n.a. Database[FooDB]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30740 Polygonum lapathifolium Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2819 Angelica sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10366 Vincetoxicum stauntonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2819 Angelica sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30740 Polygonum lapathifolium Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10366 Vincetoxicum stauntonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4460 Vincetoxicum glaucescens Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2761 Cynanchum stauntoni Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3057 Polygonum aviculare Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22715 Alpinia oxyphylla Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10366 Vincetoxicum stauntonii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14532 Salmea scandens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2819 Angelica sylvestris Species Apiaceae 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
NPO14532 Salmea scandens Oil Leaves 0.20 n.a. n.a. % PMID[37278000]
NPO14532 Salmea scandens Oil Leaves 0.16 n.a. n.a. % PMID[37278000]
NPO2819 Angelica sylvestris Oil n.a. 0.56 n.a. n.a. % PMID[37245156]
NPO3057 Polygonum aviculare Oil n.a. 0.51 n.a. n.a. % PMID[36558187]
NPO30686 Citrus hystrix Oil n.a. 0.01 n.a. n.a. % PMID[38067483]
NPO30740 Polygonum lapathifolium Oil n.a. 3.70 n.a. n.a. % PMID[36558187]
NPO45619 Myrcia sylvatica Oil Leaves 0.3 n.a. n.a. % PMID[36558108]
NPO45619 Myrcia sylvatica Oil Leaves 0.2 n.a. n.a. % PMID[36558108]
NPO45619 Myrcia sylvatica Oil Leaves 0.9 n.a. n.a. % PMID[36558108]
NPO45619 Myrcia sylvatica Oil Leaves 1.0 n.a. n.a. % PMID[36558108]
NPO45619 Myrcia sylvatica Oil Leaves 0.5 n.a. n.a. % PMID[36558108]
NPO45619 Myrcia sylvatica Oil Leaves 0.4 n.a. n.a. % PMID[36558108]
NPO46452 Eugenia luschnathiana Oil n.a. 1,44 n.a. n.a. % PMID[39292142]
NPO52082 Polygonum arenarium Oil n.a. 0.55 n.a. n.a. % PMID[36558187]
NPO56319 Polygonum persicaria Oil n.a. 0.49 n.a. n.a. % PMID[36558187]
NPO56945 Polygonum cognatum Oil n.a. 3.35 n.a. n.a. % PMID[36558187]
NPO57652 Cymbopogon flexousus Oil n.a. 0.17±0.03 n.a. n.a. % PMID[39243337]
NPO59573 Polygonum bellardii Oil n.a. 0.90 n.a. n.a. % PMID[36558187]
NPO59691 Myrtus communis subsp. tarentina n.a. n.a. 3.19 n.a. n.a. % PMID[36986980]
NPO7513 Cannabis sativa Oil n.a. 0.41 ± 0.02 n.a. n.a. % PMID[38927152]

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

In vitro activity

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

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 NPC1838 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 NPC165755
0.5909 Remote Similarity NPC294304
0.5909 Remote Similarity NPC228574

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC1838 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