Natural Product: NPC61620

Natural Product IDNPC61620
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Demethylbellidifolin
IUPAC Name 1,3,5,8-tetrahydroxyxanthen-9-one
Synonyms Bellidin; Demethylbellidifolin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL184574
PubChem CID 5281626
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones

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 MPXAWSABMVLIBU-UHFFFAOYSA-N
Standard InCHI InChI=1S/C13H8O6/c14-5-3-8(17)10-9(4-5)19-13-7(16)2-1-6(15)11(13)12(10)18/h1-4,14-17H
SMILES Oc1cc(O)c2c(c1)oc1c(c2=O)c(O)ccc1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   260.03 Volume:   242.021
?
Van der Waals volume.
Dense:   1.074 LogP:   1.449
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.702
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.191
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   17.0
TPSA:   111.13
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.362 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.607 Fsp3:   0.0
MCE-18:   18.0
?
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:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.792 Fluc inhibitor:   0.462
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.649
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.095
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.737 Promiscuous compounds:   0.894

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.663 MDCK Permeability:   -4.854
Pgp-inhibitor:   0.049 Pgp-substrate:   0.755
PAMPA:   0.593
?
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):   0.068
20% Bioavailability (F20%):   0.329 30% Bioavailability (F30%):   0.924
50% Bioavailability (F50%):   0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.009 MRP1:   0.796
Plasma Protein Binding (PPB):   94.947% Volume Distribution (VD):   -0.313
Fu: 6.894%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.497
OATP1B3 inhibitor:   0.841 BCRP inhibitor:   0.919
BSEP inhibitor:   0.601

ADMET: Metabolism

CYP1A2-inhibitor:   0.647 CYP1A2-substrate:   0.424
CYP2C19-inhibitor:   0.004 CYP2C19-substrate:   0.263
CYP2C9-inhibitor:   0.706 CYP2C9-substrate:   0.19
CYP2D6-inhibitor:   0.94 CYP2D6-substrate:   0.983
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.025
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.88
?
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):  6.237 Half-life (T1/2):  1.33

ADMET: Toxicity

hERG Blockers:  0.034 hERG Blockers (10um):  0.383
Human Hepatotoxicity (H-HT):  0.378 Drug-induced Liver Injury (DILI):  0.925
AMES Toxicity:  0.758 Rat Oral Acute Toxicity:  0.64
Maximum Recommended Daily Dose:  0.789 Skin Sensitization:  0.572
Carcinogencity:  0.796 Eye Corrosion:  0.367
Eye Irritation:  0.998 Respiratory Toxicity:  0.814
Drug-induced Neurotoxicity:  0.007 Ototoxicity:  0.05
Hematotoxicity:  0.061 Drug-induced Nephrotoxicity:  0.014
Genotoxicity:  0.985 RPMI-8226 Immunitoxicity:  0.049
A549 Cytotoxicity:  0.237 Hek293 Cytotoxicity:  0.559
BCF:   1.236
?
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:   3.661
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.468
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.909
?
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
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200490123]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200490123]
NPO19705 Gentianella campestris Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/hlca.19750580731]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/BF02675902]
NPO19150 Swertia hookeri Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(80)85027-8]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(89)80400-5]
NPO3175 Iris nigricans Species Iridaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(94)00641-6]
NPO8511 Gentiana strictiflora Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)84162-X]
NPO15376 Gentiana ramosa Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)89285-7]
NPO30126 Swertia lawii Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)98635-7]
NPO17509 Gentiana bellidifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4020(01)98434-0]
NPO30223 Swertia chirata Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(00)72792-4]
NPO30223 Swertia chirata Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(00)95355-3]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1055/s-2008-1074888]
NPO30223 Swertia chirata Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1248/cpb.30.4088]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1248/cpb.30.4088]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[10353265]
NPO2743 Swertia purpurascens Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[1133711]
NPO28502 Rhabdastrella globostellata Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[11858759]
NPO16277 Swertia davidi Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[15234768]
NPO19705 Gentianella campestris Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[15490334]
NPO28502 Rhabdastrella globostellata Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[16499318]
NPO28502 Rhabdastrella globostellata Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[16562838]
NPO28502 Rhabdastrella globostellata Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[17524651]
NPO32688 gentianella amarella ssp. acuta Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[18336006]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[18406151]
NPO28094 Consolida oliveriana Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[19489596]
NPO28502 Rhabdastrella globostellata Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[20627740]
NPO28502 Rhabdastrella globostellata Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[20718449]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[2239318]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[26996316]
NPO30433 Gentiana lacteal Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[3174858]
NPO31260 Swertia gracilescens Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[4472648]
NPO456 Swertia dilatata Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[4472648]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[4472648]
NPO30183 Swertia racemosa Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[4472648]
NPO2743 Swertia purpurascens Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[4527698]
NPO30223 Swertia chirata Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[4712626]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[5583807]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO456 Swertia dilatata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO15376 Gentiana ramosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO31260 Swertia gracilescens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO19705 Gentianella campestris Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO30223 Swertia chirata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO30432 Swertia erythrosticum Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO30183 Swertia racemosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16277 Swertia davidi Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20828 Swertia leducii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO456 Swertia dilatata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19150 Swertia hookeri Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28502 Rhabdastrella globostellata Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31260 Swertia gracilescens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30126 Swertia lawii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30183 Swertia racemosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28094 Consolida oliveriana Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31193 Gentiana campestris Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2743 Swertia purpurascens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27923 Calophyllum apetalum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30223 Swertia chirata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28996 Caloglossa leprieurii Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28366 Cladonia furcata Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO32688 gentianella amarella ssp. acuta Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28532 Streptomyces gougerotii Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO2743 Swertia purpurascens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30223 Swertia chirata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28586 Pyrus calleryana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31193 Gentiana campestris Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28457 Siler trilobum Species Salticidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15376 Gentiana ramosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28996 Caloglossa leprieurii Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28149 Polygala fallax Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28852 Euphorbia makinoi Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28586 Pyrus calleryana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28996 Caloglossa leprieurii Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2743 Swertia purpurascens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26491 Swertia nervosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19861 Drypetes molunduana Species Putranjivaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19705 Gentianella campestris Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15376 Gentiana ramosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20828 Swertia leducii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28457 Siler trilobum Species Salticidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30223 Swertia chirata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31193 Gentiana campestris Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28586 Pyrus calleryana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20828 Swertia leducii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28020 Hypaphorus subumbrans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15376 Gentiana ramosa Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8511 Gentiana strictiflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28502 Rhabdastrella globostellata Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28011 Swertia japonica Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19150 Swertia hookeri Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20828 Swertia leducii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28252 Lophozia barbata Species Scapaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19861 Drypetes molunduana Species Putranjivaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28094 Consolida oliveriana Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17509 Gentiana bellidifolia Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28996 Caloglossa leprieurii Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19705 Gentianella campestris Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28793 Wettsteinia inversa Species Adelanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20937 Heterocapsa niei Species Heterocapsaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28532 Streptomyces gougerotii Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO27923 Calophyllum apetalum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2355 Swertia macrosperma Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29129 Rhodiola heterodonta Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28417 Monnina emarginata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28366 Cladonia furcata Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22057 Gentiana kochiana Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28852 Euphorbia makinoi Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28586 Pyrus calleryana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16277 Swertia davidi Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28457 Siler trilobum Species Salticidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO456 Swertia dilatata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28149 Polygala fallax Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3175 Iris nigricans Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2743 Swertia purpurascens Species Gentianaceae 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

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 = 13000.0 nM PMID[15482934]
NPT204 Individual protein Acetylcholinesterase Homo sapiens Inhibition = 17.5 % PMID[18336006]
NPT261 Individual protein Monoamine oxidase A Homo sapiens Inhibition = 90.5 % PMID[18336006]
NPT1682 Individual protein Dual specificity protein kinase CLK2 Homo sapiens IC50 = 1697.0 nM PMID[36876904]
NPT3231 Individual protein Dual specificity protein kinase CLK4 Homo sapiens IC50 = 146.3 nM PMID[36876904]
NPT3459 Individual protein Dual specificity tyrosine-phosphorylation-regulated kinase 4 Homo sapiens IC50 > 10000.0 nM PMID[36876904]
NPT1683 Individual protein Dual specificity protein kinase CLK3 Homo sapiens IC50 = 7530.0 nM PMID[36876904]
NPT3114 Individual protein Dual-specificity tyrosine-phosphorylation regulated kinase 1A Homo sapiens TIME = 0.014 hr PMID[36876904]
NPT3274 Individual protein Dual specificity tyrosine-phosphorylation-regulated kinase 1B Homo sapiens IC50 = 268.3 nM PMID[36876904]
NPT3114 Individual protein Dual-specificity tyrosine-phosphorylation regulated kinase 1A Homo sapiens IC50 = 266.1 nM PMID[36876904]
NPT3114 Individual protein Dual-specificity tyrosine-phosphorylation regulated kinase 1A Homo sapiens Kd = 60.02 nM PMID[36876904]
NPT3460 Individual protein Dual-specificity tyrosine-phosphorylation regulated kinase 3 Homo sapiens IC50 > 10000.0 nM PMID[36876904]
NPT3399 Individual protein Dual-specificity tyrosine-phosphorylation regulated kinase 2 Homo sapiens IC50 = 2713.0 nM PMID[36876904]
NPT3226 Individual protein Casein kinase I epsilon Homo sapiens IC50 > 10000.0 nM PMID[36876904]
NPT582 Individual protein Monoamine oxidase B Homo sapiens Inhibition = 59.0 % PMID[18336006]
NPT1509 Protein complex Cyclin-dependent kinase 5/CDK5 activator 1 Homo sapiens IC50 = 200.0 nM PMID[21353545]
NPT29648 Single protein Dual specificity protein kinase CLK1 Homo sapiens IC50 = 238.8 nM PMID[36876904]
NPT29648 Single protein Dual specificity protein kinase CLK1 Homo sapiens Kd = 29.74 nM PMID[36876904]
NPT29648 Single protein Dual specificity protein kinase CLK1 Homo sapiens TIME = 0.004333 hr PMID[36876904]
NPT497 Individual protein Maltase-glucoamylase Homo sapiens IC50 = 5300.0 nM PMID[30282319]
NPT497 Individual protein Maltase-glucoamylase Homo sapiens IC50 = 5200.0 nM PMID[30282319]
NPT591 Individual protein Glycogen synthase kinase-3 beta Homo sapiens Activity n.a. n.a. n.a. PMID[36876904]
NPT591 Individual protein Glycogen synthase kinase-3 beta Homo sapiens IC50 > 10000.0 nM PMID[36876904]
NPT591 Individual protein Glycogen synthase kinase-3 beta Homo sapiens Kd > 10000.0 nM PMID[36876904]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT76 Cell line C6 Rattus norvegicus IC50 > 100000.0 nM PMID[18406151]
NPT380 Cell line U-251 Homo sapiens IC50 > 100000.0 nM PMID[18406151]
NPT804 Cell line HT-22 Mus musculus IC50 = 2500.0 nM PMID[36876904]
NPT28438 Unchecked Unchecked n.a. Ratio IC50 > 3.0 n.a. PMID[36876904]
NPT28438 Unchecked Unchecked n.a. Ratio IC50 = 0.9 n.a. PMID[36876904]
NPT28438 Unchecked Unchecked n.a. Ratio IC50 = 1.01 n.a. PMID[36876904]
NPT30024 Protein complex Cyclin-dependent kinase 5/CDK5 activator 1 Homo sapiens IC50 > 10000.0 nM PMID[36876904]
NPT2 Others Unspecified n.a. IC50 > 50000.0 nM PMID[18406151]

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 NPC61620 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
0.7111 Intermediate Similarity NPC272721
0.6981 Remote Similarity NPC272560
0.6042 Remote Similarity NPC196277
0.5957 Remote Similarity NPC169479
0.5957 Remote Similarity NPC276930
0.58 Remote Similarity NPC199100
0.5745 Remote Similarity NPC194856
0.549 Remote Similarity NPC151473
0.5435 Remote Similarity NPC610063
0.5306 Remote Similarity NPC239495
0.5306 Remote Similarity NPC275734
0.5192 Remote Similarity NPC265251
0.5098 Remote Similarity NPC202157

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC61620 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