Natural Product: NPC123259

Natural Product IDNPC123259
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Punicalin
IUPAC Name n.a.
Synonyms Pumcalin; Punicalin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL502440
PubChem CID 5464368
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000238] Tannins
        • [CHEMONTID:0001710] Hydrolyzable tannins

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 IQHIEHIKNWLKFB-ITTSEVFZSA-N
Standard InCHI InChI=1S/C34H22O22/c35-6-1-4-9(19(39)17(6)37)11-15-13-14-16(33(50)56-28(13)23(43)21(11)41)12(22(42)24(44)29(14)55-32(15)49)10-5(2-7(36)18(38)20(10)40)31(48)54-27-8(3-52-30(4)47)53-34(51)26(46)25(27)45/h1-2,8,25-27,34-46,51H,3H2/t8-,25-,26-,27-,34-/m1/s1
SMILES O[C@@H]1O[C@@H]2COC(=O)c3cc(O)c(c(c3c3c(O)c(O)c4c5c3c(=O)oc3c(c(c(c6c(C(=O)O[C@H]2[C@@H]([C@H]1O)O)cc(O)c(c6O)O)c(c(=O)o4)c53)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   782.06 Volume:   679.37
?
Van der Waals volume.
Dense:   1.151 LogP:   -0.759
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -1.145
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.799
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   50.0
TPSA:   385.24
?
Topological Polar Surface Area.
 H-Bond Acceptor:   22.0
H-Bond Donor:   13.0 Rings:   8.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.042 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.888 Fsp3:   0.176
MCE-18:   181.5
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.913 Fluc inhibitor:   0.07
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.05
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.662
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.285 Promiscuous compounds:   0.987

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.822 MDCK Permeability:   -4.968
Pgp-inhibitor:   0.0 Pgp-substrate:   0.724
PAMPA:   1.0
?
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):   0.001
20% Bioavailability (F20%):   0.053 30% Bioavailability (F30%):   0.976
50% Bioavailability (F50%):   0.966

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.999
Plasma Protein Binding (PPB):   85.681% Volume Distribution (VD):   -0.101
Fu: 12.131%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.008
BSEP inhibitor:   0.001

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.085
CYP2C9-inhibitor:   0.35 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.164
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.097
?
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):  3.226 Half-life (T1/2):  5.311

ADMET: Toxicity

hERG Blockers:  0.003 hERG Blockers (10um):  0.241
Human Hepatotoxicity (H-HT):  0.811 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.978 Rat Oral Acute Toxicity:  0.159
Maximum Recommended Daily Dose:  0.937 Skin Sensitization:  1.0
Carcinogencity:  0.394 Eye Corrosion:  0.0
Eye Irritation:  0.923 Respiratory Toxicity:  0.01
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.989
Hematotoxicity:  0.108 Drug-induced Nephrotoxicity:  0.633
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.042
A549 Cytotoxicity:  0.98 Hek293 Cytotoxicity:  0.151
BCF:   0.675
?
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:   3.361
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.655
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.398
?
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
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. fruit n.a. DOI[10.1007/s00217-007-0799-1]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. flower n.a. DOI[10.1016/j.foodchem.2011.01.077]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[11520216]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. PMID[11520216]
NPO20652 Phytolacca acinosa Species Phytolaccaceae Eukaryota n.a. n.a. n.a. PMID[12932140]
NPO21349 Punica granatum Species Lythraceae Eukaryota Seeds n.a. n.a. PMID[15620261]
NPO20779 Garcinia hombroniana Species Clusiaceae Eukaryota leaves n.a. n.a. PMID[16124765]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[20121251]
NPO20842 Beauveria felina Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[21438588]
NPO20146 Cladiella krempfi Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[21861494]
NPO20096 Cirsium japonicum Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[21899269]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22612410]
NPO20842 Beauveria felina Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[23822585]
NPO20842 Beauveria felina Species Cordycipitaceae Eukaryota n.a. n.a. n.a. PMID[26295595]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[36560643]
NPO16414 Thuja plicata Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[36985451]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38792265]
NPO16414 Thuja plicata Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[38794396]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[39138188]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[39527985]
NPO22052 Aspergillus candidus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[5391291]
NPO20972 Oscillatoria princeps Species Oscillatoriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19899 Crepis foetida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22121 Piper arboreum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22568 Aristolochia elegans Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21227 Aglaia elaeagnoidea Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21282 Aplidium orthium Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22893 Apterostigma dentigerum Species Formicidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22052 Aspergillus candidus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28912 Astragalus gummifer Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20842 Beauveria felina Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2780 Brenneria rubrifaciens Species Pectobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO21096 Cardiospermum halicacabum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21859 Centaurea nigrescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20096 Cirsium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20146 Cladiella krempfi Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12362 Coreopsis fasciculata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23010 Crinum defixum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22763 Cuphea carthagenensis Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20332 Dioscoreophyllum cumminsii Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20209 Dorstenia lindeniana Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21603 Eskemukerjea megacarpum n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO22381 Euphorbia segetalis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20779 Garcinia hombroniana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21991 Modiolus demissus Species Mytilidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22829 Ozoroa insignis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22250 Parastrephia lepidophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22635 Penstemon secundiflorus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6395 Phedimus kamtschaticus Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22315 Phlogacanthus thyrsiflorus Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21420 Phormia regina Species Calliphoridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20652 Phytolacca acinosa Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21730 Pouzolzia occidentalis Species Urticaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22976 Ruta microcarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13355 Selinum carvifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22447 Sidastrum acuminatum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22509 Syncolostemon parviflorus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16414 Thuja plicata Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29466 Triglochin maritima Species Juncaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21473 Urtica triangularis Species Urticaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23953 Zanthoxylum monophyllum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Root Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Stem Bark n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota Twig n.a. n.a. Database[FooDB]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[FooDB]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20096 Cirsium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22976 Ruta microcarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16414 Thuja plicata Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21096 Cardiospermum halicacabum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO21349 Punica granatum Species Lythraceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO6395 Phedimus kamtschaticus Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20652 Phytolacca acinosa Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29466 Triglochin maritima Species Juncaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22976 Ruta microcarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16414 Thuja plicata Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20096 Cirsium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21096 Cardiospermum halicacabum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22121 Piper arboreum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20096 Cirsium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21096 Cardiospermum halicacabum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20652 Phytolacca acinosa Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22976 Ruta microcarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20096 Cirsium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20652 Phytolacca acinosa Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28912 Astragalus gummifer Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22447 Sidastrum acuminatum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23953 Zanthoxylum monophyllum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21859 Centaurea nigrescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21730 Pouzolzia occidentalis Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23010 Crinum defixum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22568 Aristolochia elegans Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20652 Phytolacca acinosa Species Phytolaccaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21227 Aglaia elaeagnoidea Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20209 Dorstenia lindeniana Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20146 Cladiella krempfi Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21473 Urtica triangularis Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20842 Beauveria felina Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16414 Thuja plicata Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22250 Parastrephia lepidophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20779 Garcinia hombroniana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6395 Phedimus kamtschaticus Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22635 Penstemon secundiflorus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21603 Eskemukerjea megacarpum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20096 Cirsium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22829 Ozoroa insignis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21096 Cardiospermum halicacabum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20332 Dioscoreophyllum cumminsii Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20972 Oscillatoria princeps Species Oscillatoriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22976 Ruta microcarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13355 Selinum carvifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22052 Aspergillus candidus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21282 Aplidium orthium Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22509 Syncolostemon parviflorus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22121 Piper arboreum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21349 Punica granatum Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22315 Phlogacanthus thyrsiflorus Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22893 Apterostigma dentigerum Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22763 Cuphea carthagenensis Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19899 Crepis foetida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22381 Euphorbia segetalis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29466 Triglochin maritima Species Juncaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21991 Modiolus demissus Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28912 Astragalus gummifer Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21420 Phormia regina Species Calliphoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12362 Coreopsis fasciculata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2780 Brenneria rubrifaciens Species Pectobacteriaceae Bacteria 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
NPT326 Individual protein Squalene monooxygenase Rattus norvegicus IC50 = 20000.0 nM PMID[11520216]
NPT459 Individual protein Human immunodeficiency virus type 1 reverse transcriptase Human immunodeficiency virus 1 ID50 = 8.0 uM PMID[1698933]
NPT459 Individual protein Human immunodeficiency virus type 1 reverse transcriptase Human immunodeficiency virus 1 Activity = 11.4 % PMID[1698933]
NPT459 Individual protein Human immunodeficiency virus type 1 reverse transcriptase Human immunodeficiency virus 1 Activity = 34.4 % PMID[1698933]
NPT459 Individual protein Human immunodeficiency virus type 1 reverse transcriptase Human immunodeficiency virus 1 Activity = 45.3 % PMID[1698933]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT759 Cell line H9 Homo sapiens GI = 15.0 % PMID[1698933]
NPT672 Cell line TE-671 Homo sapiens ED50 > 10.0 ug ml-1 PMID[1431932]
NPT180 Cell line HCT-8 Homo sapiens ED50 > 10.0 ug ml-1 PMID[1431932]
NPT81 Cell line A549 Homo sapiens ED50 > 10.0 ug ml-1 PMID[1431932]
NPT91 Cell line KB Homo sapiens ED50 > 10.0 ug ml-1 PMID[1431932]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. ED50 > 10.0 ug ml-1 PMID[1431932]
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 Inhibition > 50.0 % PMID[1698933]
NPT2 Others Unspecified n.a. Activity = 109.0 % PMID[2413172]
NPT2 Others Unspecified n.a. Activity = 105.0 % PMID[2413172]
NPT2 Others Unspecified n.a. Activity = 1.0 % PMID[2413172]
NPT2 Others Unspecified n.a. Activity = 8.0 % PMID[2413172]
NPT2 Others Unspecified n.a. Activity = 35.0 % PMID[2413172]
NPT2 Others Unspecified n.a. Activity = 62.0 % PMID[2413172]
NPT2 Others Unspecified n.a. Activity = 119.0 % PMID[2413172]
NPT2 Others Unspecified n.a. Activity = 64.0 % PMID[2413172]
NPT2 Others Unspecified n.a. Activity = 31.0 % PMID[2413172]
NPT2 Others Unspecified n.a. Activity = 6.0 % PMID[2413172]

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 NPC123259 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 NPC129533
0.8462 Intermediate Similarity NPC486112
0.7595 Intermediate Similarity NPC486113
0.7179 Intermediate Similarity NPC237202
0.7174 Intermediate Similarity NPC486111
0.618 Remote Similarity NPC269046
0.5955 Remote Similarity NPC125352
0.5446 Remote Similarity NPC486110
0.5385 Remote Similarity NPC488888

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC123259 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