Natural Product: NPC567521

Natural Product IDNPC567521
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 9-[(2~{R},3~{R},4~{S},5~{S})-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-3~{H}-purine-2,6-dione
IUPAC Name 9-[(2~{R},3~{R},4~{S},5~{S})-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-3~{H}-purine-2,6-dione
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 UBORTCNDUKBEOP-HAVMAKPUSA-N
Standard InCHI InChI=1S/C10H12N4O6/c15-1-3-5(16)6(17)9(20-3)14-2-11-4-7(14)12-10(19)13-8(4)18/h2-3,5-6,9,15-17H,1H2,(H2,12,13,18,19)/t3-,5+,6+,9+/m0/s1
SMILES O=C1NC(=O)C2=C(N1)N([C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O)C=N2

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   284.08 Volume:   242.03
?
Van der Waals volume.
Dense:   1.174 LogP:   -1.636
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.884
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.72
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   17.0
TPSA:   153.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.394 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.781 Fsp3:   0.5
MCE-18:   63.6
?
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:   0.012 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.235
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.02
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.039 Promiscuous compounds:   0.033

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.999 MDCK Permeability:   -5.398
Pgp-inhibitor:   0.013 Pgp-substrate:   0.636
PAMPA:   0.997
?
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):   0.808
20% Bioavailability (F20%):   0.033 30% Bioavailability (F30%):   0.786
50% Bioavailability (F50%):   0.947

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.256
Plasma Protein Binding (PPB):   25.689% Volume Distribution (VD):   -0.263
Fu: 70.457%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.988
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.342
BSEP inhibitor:   0.19

ADMET: Metabolism

CYP1A2-inhibitor:   0.012 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.076 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.002
HLM stability:   0.021
?
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):  5.533 Half-life (T1/2):  2.234

ADMET: Toxicity

hERG Blockers:  0.012 hERG Blockers (10um):  0.15
Human Hepatotoxicity (H-HT):  0.723 Drug-induced Liver Injury (DILI):  0.983
AMES Toxicity:  0.446 Rat Oral Acute Toxicity:  0.183
Maximum Recommended Daily Dose:  0.03 Skin Sensitization:  0.076
Carcinogencity:  0.136 Eye Corrosion:  0.0
Eye Irritation:  0.165 Respiratory Toxicity:  0.176
Drug-induced Neurotoxicity:  0.807 Ototoxicity:  0.911
Hematotoxicity:  0.556 Drug-induced Nephrotoxicity:  0.878
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.029
A549 Cytotoxicity:  0.014 Hek293 Cytotoxicity:  0.04
BCF:   -0.029
?
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:   1.983
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.624
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.583
?
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
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[ 16712885]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1016/0006-291X(79)91731-5]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.foodchem.2013.08.121]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)00169-2]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(99)00119-3]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1093/emboj/18.8.2021]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1091286]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[10977898]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1100617]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11745165]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11750815]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12369847]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12467448]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12805358]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. ChEBI[131529]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13610867]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13831814]
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. seed n.a. PMID[14640528]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[14973046]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15031653]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. fruit n.a. PMID[15128023]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15292242]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15610037]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Flowers n.a. n.a. PMID[16180814]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1644759]
NPO8258 Camellia sinensis Species Theaceae Eukaryota seeds Shizuoka prefecture, Japan n.a. PMID[16499314]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[16630633]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[170247]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[17765195]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[179975]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[18068204]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[18068204]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota leaves Mato Leitao, RS, Brazil n.a. PMID[18192087]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19026742]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19514719]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19561621]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[21434603]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21437340]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. flower n.a. PMID[21922925]
NPO8258 Camellia sinensis Species Theaceae Eukaryota flower buds n.a. n.a. PMID[21925888]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21988831]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22289691]
NPO8258 Camellia sinensis Species Theaceae Eukaryota leaves n.a. n.a. PMID[22377672]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22855027]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. leaf n.a. PMID[23265489]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23537328]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaves Bandung, West Java, Indonesia PMID[23621359]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23676670]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[241475]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24206068]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24783849]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24831709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24939187]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24966042]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24967680]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[2543976]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[25867074]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. PMID[25955847]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26195826]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26337258]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26670289]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26826371]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29897754]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30302998]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[318639]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[3283102]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[37049761]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[37255739]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[398096]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4877125]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4879561]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4908789]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[5332408]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6102982]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6284709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6338507]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7042909]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7601837]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[8852895]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[9470222]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO320 Coffea canephora Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO55421 FOOD SAKE n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO21254 Paullinia cupana Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44163 Cammellia assamica var.kucha n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO61375 Coffea dewevrei Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24402 Coffea liberica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO60414 Herreania sp. n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44221 Coffea racemosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO47654 Coffea salvatrix Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO55348 Camellia irrawadiensisia Genus Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO43215 Camellia kissi Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO46714 Camellia ptilophylla Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO46207 Camellia taliensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO52823 Camellia toliensis Genus Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO53706 Coffea eugeniodes Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO57761 Coffea kianjavatensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO50287 Cola sp. Genus Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO55944 Camellia assamica Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO320 Coffea canephora Species Rubiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaf Essent. Oil 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]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Seed Oil n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. Database[FooDB]
NPO24402 Coffea liberica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21254 Paullinia cupana Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[https://doi.org/10.1016/j.jbiosc.2016.12.008]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24402 Coffea liberica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO320 Coffea canephora Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21254 Paullinia cupana Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO320 Coffea canephora Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21254 Paullinia cupana Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29456 Theobroma grandiflorum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24402 Coffea liberica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26571 Ilex paraguariensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9788 Coffea arabica Species Rubiaceae 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

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 NPC567521 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
0.6 Remote Similarity NPC487897
0.5484 Remote Similarity NPC61198

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC567521 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
0.5484 Remote Similarity NPD252 Clinical (unspecified phase)
0.5484 Remote Similarity NPD549 Phase 4

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