NPASS Compound

Natural Product: NPC109887

Natural Product ID	NPC109887
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Purginoside Iv
IUPAC Name	n.a.
Synonyms	Purginoside IV
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2336639
PubChem CID	71719497
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

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

Chemical Representations

RDKit 2D 195200 0 0 0 0 0 0 0 0999 V2000 15.0597 8.3428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.9107 7.3786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.7616 6.4144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.6125 5.4502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4635 4.4861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3144 3.5219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1653 2.5577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0163 1.5935 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8672 0.6293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7181 -0.3349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2566 0.0025 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9786 -1.8121 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8296 -2.7762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4200 -3.2893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1595 -4.7665 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3086 -5.7307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7181 -5.2176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9786 -3.7404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3882 -4.2535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.5372 -3.2893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2872 -4.5883 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7872 -4.5883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1968 -5.1013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.6063 -5.6144 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.5372 -3.2893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7872 -1.9902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2872 -1.9902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8777 -1.4772 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5268 -0.5130 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.6863 -2.3251 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9786 -6.6949 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3882 -7.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6382 -8.5069 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3882 -9.8060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6486 -11.2832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8882 -9.8060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6382 -8.5069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8882 -7.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6277 -5.7307 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7872 -7.5427 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.2977 -10.3190 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5582 -11.7962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4091 -12.7604 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.9677 -12.3092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.3772 -12.8223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.7868 -13.3353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.1963 -13.8483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.6059 -14.3614 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1595 -6.6949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1595 -1.8121 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6491 0.9642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 1.2990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4895 -2.7762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6491 -0.9642 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0586 -1.4772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7981 -2.9544 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5586 -1.4772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9681 -0.9642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1172 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8672 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1277 2.7762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8672 4.2535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1172 5.5525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9681 6.5167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5586 7.0297 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0586 7.0297 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6491 6.5167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 5.5525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 4.2535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4895 2.7762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 4.2535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1595 3.7404 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 5.5525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 6.8515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 6.8515 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4895 8.3287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6491 6.5167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0292 8.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9999 9.2118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9705 10.3029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0588 11.3940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0882 12.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.2088 9.3070 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 16.0239 7.1937 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.0956 9.4918 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 14.8749 6.2295 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 12.9465 8.5277 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 11.7974 7.5635 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 13.7258 5.2653 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 12.5767 4.3012 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.6484 6.5993 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4993 5.6351 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 11.4277 3.3370 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2786 2.3728 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3502 4.6709 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2012 3.7068 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1295 1.4086 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0521 2.7426 0.0000 H 0 0 0 0 0 0 0 0 0 0 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58 1 0 56 59 1 0 59 60 1 0 60 61 2 0 60 62 1 0 62 63 1 0 63 64 1 0 64 65 1 0 65 66 1 0 66 67 1 0 67 68 1 0 68 69 1 0 69 70 1 0 70 71 1 0 71 72 1 0 72 73 1 0 73 74 1 0 74 75 1 0 74 76 1 0 76 77 1 0 76 78 1 0 78 79 1 0 79 80 1 0 79 81 1 0 78 82 1 0 71 83 1 0 83 84 1 0 84 85 1 0 85 86 1 0 86 87 1 0 18 13 1 0 27 20 1 0 38 32 1 0 57 51 1 0 80 73 1 0 75 55 1 0 1 88 1 0 1 89 1 0 1 90 1 0 2 91 1 0 2 92 1 0 3 93 1 0 3 94 1 0 4 95 1 0 4 96 1 0 5 97 1 0 5 98 1 0 6 99 1 0 6100 1 0 7101 1 0 7102 1 0 8103 1 0 8104 1 0 9105 1 0 9106 1 0 13107 1 1 14108 1 6 16109 1 1 17110 1 6 18111 1 1 20112 1 6 22113 1 6 23114 1 0 23115 1 0 24116 1 0 25117 1 1 26118 1 6 27119 1 1 28120 1 0 29121 1 0 30122 1 0 32123 1 6 34124 1 1 35125 1 0 35126 1 0 35127 1 0 36128 1 6 37129 1 1 38130 1 1 39131 1 0 40132 1 0 44133 1 0 44134 1 0 45135 1 0 45136 1 0 46137 1 0 46138 1 0 47139 1 0 47140 1 0 48141 1 0 48142 1 0 48143 1 0 49144 1 0 49145 1 0 49146 1 0 51147 1 1 52148 1 6 53149 1 0 53150 1 0 53151 1 0 55152 1 1 56153 1 6 57154 1 6 58155 1 0 62156 1 0 62157 1 0 63158 1 0 63159 1 0 64160 1 0 64161 1 0 65162 1 0 65163 1 0 66164 1 0 66165 1 0 67166 1 0 67167 1 0 68168 1 0 68169 1 0 69170 1 0 69171 1 0 70172 1 0 70173 1 0 71174 1 1 73175 1 1 74176 1 6 76177 1 1 77178 1 0 78179 1 1 79180 1 1 81181 1 0 81182 1 0 81183 1 0 82184 1 0 83185 1 0 83186 1 0 84187 1 0 84188 1 0 85189 1 0 85190 1 0 86191 1 0 86192 1 0 87193 1 0 87194 1 0 87195 1 0 M END

Standard InCHIKey	ITHWOIDZLGRETC-RBIFCKFXSA-N
Standard InCHI	InChI=1S/C62H108O25/c1-8-11-14-15-17-21-27-32-42(66)83-57-56(87-59-48(72)45(69)44(68)39(33-63)80-59)53(85-58-49(73)47(71)51(35(5)76-58)81-40(64)30-24-13-10-3)37(7)78-62(57)84-52-36(6)77-61-55(50(52)74)82-41(65)31-26-22-19-16-18-20-25-29-38(28-23-12-9-2)79-60-54(86-61)46(70)43(67)34(4)75-60/h34-39,43-63,67-74H,8-33H2,1-7H3/t34-,35+,36+,37+,38+,39-,43+,44-,45+,46+,47+,48-,49-,50-,51+,52+,53+,54-,55-,56-,57-,58+,59+,60+,61+,62+/m1/s1
SMILES	CCCCCCCCCC(=O)O[C@H]1[C@@H](O[C@H]([C@@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)OC(=O)CCCCC)C)O[C@H]1[C@H](C)O[C@@H]2[C@@H]([C@@H]1O)OC(=O)CCCCCCCCC[C@@H](O[C@H]1[C@H](O2)[C@@H](O)[C@H]([C@H](O1)C)O)CCCCC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1252.72	Volume:	1241.415 ? Van der Waals volume.
Dense:	1.009	LogP:	4.509 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.5 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.88 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	27.0	Rigid Bonds:	49.0
TPSA:	353.27 ? Topological Polar Surface Area.	H-Bond Acceptor:	25.0
H-Bond Donor:	9.0	Rings:	6.0
Heavy Atoms:	25.0

MedChem Properties

QED Drug-Likeness Score:	0.035	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.272	Fsp³:	0.952
MCE-18:	121.19 ? 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:	0	PAINS Alert:	0
Colloidal aggregators:	0.997	Fluc inhibitor:	0.333 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.001 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.551	Promiscuous compounds:	0.105

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.564	MDCK Permeability:	-5.091
Pgp-inhibitor:	0.0	Pgp-substrate:	0.967
PAMPA:	0.985 ? 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):	0.125
20% Bioavailability (F20%):	0.006	30% Bioavailability (F30%):	0.818
50% Bioavailability (F50%):	0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.984
Plasma Protein Binding (PPB):	93.14%	Volume Distribution (VD):	-0.06
Fu:	4.874% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.986
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.146

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	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:	0.041
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.896 ? 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):

0.769

Half-life (T1/2):

3.023

ADMET: Toxicity

hERG Blockers:	0.026	hERG Blockers (10um):	0.094
Human Hepatotoxicity (H-HT):	0.425	Drug-induced Liver Injury (DILI):	0.986
AMES Toxicity:	0.577	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.001	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.626	Drug-induced Nephrotoxicity:	0.971
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.548
A549 Cytotoxicity:	0.999	Hek293 Cytotoxicity:	0.331
BCF:	0.672 ? 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:	4.43 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.068 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.802 ? 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
NPO19106	Ipomoea purga	Species	Convolvulaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21446661]
NPO19106	Ipomoea purga	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23273047]
NPO19106	Ipomoea purga	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19106	Ipomoea purga	Species	Convolvulaceae	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

Activity Type	# Activity
FC	3
IC50	2

Activity Type	# Activity
Cell line	3
Individual protein	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	FC	=	3.3	n.a.	DOI[10.1007/s00044-013-0839-2]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	FC	=	3.0	n.a.	PMID[16854066]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	25.0	ug.mL-1	PMID[10654414]
NPT83	Cell line	MCF7	Homo sapiens	FC	=	2.5	n.a.	PMID[19296616]

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

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 NPC109887 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	24022
0.1-0.2	21856
0.2-0.3	3440
0.3-0.4	381
0.4-0.5	38
0.5-0.6	40
0.6-0.7	36
0.7-0.8	0
0.8-0.85	6
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.875	High Similarity	NPC224953
0.8333	Intermediate Similarity	NPC477326
0.8219	Intermediate Similarity	NPC478729
0.8101	Intermediate Similarity	NPC600446
0.8101	Intermediate Similarity	NPC605013
0.8072	Intermediate Similarity	NPC184915
0.8026	Intermediate Similarity	NPC477330
0.7927	Intermediate Similarity	NPC119583
0.7922	Intermediate Similarity	NPC477329
0.7882	Intermediate Similarity	NPC44782
0.7831	Intermediate Similarity	NPC483170
0.7792	Intermediate Similarity	NPC477328
0.7738	Intermediate Similarity	NPC115013
0.7733	Intermediate Similarity	NPC606819
0.7647	Intermediate Similarity	NPC183888
0.7625	Intermediate Similarity	NPC604005
0.7625	Intermediate Similarity	NPC605014
0.7558	Intermediate Similarity	NPC472200
0.7532	Intermediate Similarity	NPC477350
0.7531	Intermediate Similarity	NPC89843
0.75	Intermediate Similarity	NPC113745
0.75	Intermediate Similarity	NPC477320
0.75	Intermediate Similarity	NPC477323
0.75	Intermediate Similarity	NPC477325
0.75	Intermediate Similarity	NPC609436
0.7468	Intermediate Similarity	NPC281563
0.7442	Intermediate Similarity	NPC126685
0.7439	Intermediate Similarity	NPC477344
0.7326	Intermediate Similarity	NPC169345
0.7317	Intermediate Similarity	NPC478734
0.7317	Intermediate Similarity	NPC477331
0.7317	Intermediate Similarity	NPC477332
0.7312	Intermediate Similarity	NPC28069
0.7312	Intermediate Similarity	NPC77651
0.7191	Intermediate Similarity	NPC478728
0.7143	Intermediate Similarity	NPC478733
0.7126	Intermediate Similarity	NPC477317
0.7126	Intermediate Similarity	NPC477318
0.7111	Intermediate Similarity	NPC478727
0.7059	Intermediate Similarity	NPC478722
0.7059	Intermediate Similarity	NPC479061
0.7059	Intermediate Similarity	NPC267592
0.7059	Intermediate Similarity	NPC478725
0.7045	Intermediate Similarity	NPC259294
0.7	Intermediate Similarity	NPC146380
0.6977	Remote Similarity	NPC297768
0.6977	Remote Similarity	NPC478723
0.6977	Remote Similarity	NPC478724
0.6977	Remote Similarity	NPC479060
0.6907	Remote Similarity	NPC290276
0.6897	Remote Similarity	NPC307400
0.6897	Remote Similarity	NPC472204
0.6897	Remote Similarity	NPC27289
0.6867	Remote Similarity	NPC22742
0.6867	Remote Similarity	NPC477349
0.6867	Remote Similarity	NPC477346
0.6818	Remote Similarity	NPC238264
0.6818	Remote Similarity	NPC478726
0.6818	Remote Similarity	NPC477345
0.6782	Remote Similarity	NPC477319
0.6768	Remote Similarity	NPC471025
0.6705	Remote Similarity	NPC143421
0.6667	Remote Similarity	NPC146992
0.6667	Remote Similarity	NPC85759
0.6593	Remote Similarity	NPC123204
0.6574	Remote Similarity	NPC147032
0.6556	Remote Similarity	NPC290012
0.6517	Remote Similarity	NPC294748
0.6505	Remote Similarity	NPC471026
0.6413	Remote Similarity	NPC163409
0.6404	Remote Similarity	NPC472205
0.6381	Remote Similarity	NPC471024
0.6374	Remote Similarity	NPC238056
0.625	Remote Similarity	NPC475241
0.6238	Remote Similarity	NPC10883
0.6196	Remote Similarity	NPC478731
0.6154	Remote Similarity	NPC478730
0.6087	Remote Similarity	NPC476087
0.6087	Remote Similarity	NPC475667
0.6067	Remote Similarity	NPC479059
0.6022	Remote Similarity	NPC478732
0.5957	Remote Similarity	NPC475270
0.5957	Remote Similarity	NPC475327
0.5946	Remote Similarity	NPC206823
0.5934	Remote Similarity	NPC60849
0.5922	Remote Similarity	NPC611287
0.5895	Remote Similarity	NPC475525
0.5895	Remote Similarity	NPC475540
0.5833	Remote Similarity	NPC476066
0.5833	Remote Similarity	NPC269318
0.5814	Remote Similarity	NPC475425
0.5794	Remote Similarity	NPC600940
0.5773	Remote Similarity	NPC475164
0.5769	Remote Similarity	NPC10121
0.5769	Remote Similarity	NPC198918
0.5714	Remote Similarity	NPC473605
0.5714	Remote Similarity	NPC475375
0.5714	Remote Similarity	NPC600672
0.5714	Remote Similarity	NPC610996
0.5699	Remote Similarity	NPC173328
0.5638	Remote Similarity	NPC186992
0.5596	Remote Similarity	NPC472352
0.5556	Remote Similarity	NPC87153
0.5543	Remote Similarity	NPC158302
0.5532	Remote Similarity	NPC479058
0.5521	Remote Similarity	NPC162925
0.551	Remote Similarity	NPC477347
0.5505	Remote Similarity	NPC610997
0.55	Remote Similarity	NPC477348
0.5463	Remote Similarity	NPC600721
0.5463	Remote Similarity	NPC605872
0.5437	Remote Similarity	NPC124878
0.5437	Remote Similarity	NPC231888
0.5385	Remote Similarity	NPC35338
0.5385	Remote Similarity	NPC204214
0.5385	Remote Similarity	NPC92283
0.5306	Remote Similarity	NPC479057
0.5238	Remote Similarity	NPC63404
0.5208	Remote Similarity	NPC44682
0.5053	Remote Similarity	NPC216883
0.5052	Remote Similarity	NPC476781

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC109887 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7435
0.1-0.2	1622
0.2-0.3	89
0.3-0.4	4
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

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