NPASS Compound

Natural Product: NPC72016

Natural Product ID	NPC72016
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Kaempferol 3-O-(5-O-Acetyl-Alpha-D-Apiofuranosyl)-7-O-Alpha-L-Rhamnopyranoside
IUPAC Name	[(3R,4S,5R)-3,4-dihydroxy-5-[5-hydroxy-2-(4-hydroxyphenyl)-4-oxo-7-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxychromen-3-yl]oxyoxolan-3-yl]methyl acetate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1929025
PubChem CID	25067894
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-glycosides

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

Chemical Representations

RDKit 3D 73 77 0 0 0 0 0 0 0 0999 V2000 8.0104 3.4035 -2.4033 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6214 1.9789 -2.3391 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8218 1.2509 -3.3530 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0437 1.4279 -1.1937 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6744 0.0678 -1.1380 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0862 -0.1943 0.2267 C 0 0 2 0 0 0 0 0 0 0 0 0 7.0279 0.0846 1.2023 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6164 -1.6365 0.3591 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5840 -1.5629 1.2708 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8221 -0.5017 0.8633 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8040 0.5597 0.4503 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9481 1.4950 1.4835 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9867 -0.7724 -0.2694 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6055 -0.5827 -0.1796 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7881 -1.6261 0.1358 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5092 -1.3524 0.2161 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0589 -0.1950 0.0201 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2590 0.8879 -0.3059 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0898 0.6944 -0.4078 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8508 1.6332 -0.6981 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8682 2.1050 -0.5089 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0272 3.1631 -0.8340 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2227 2.2328 -0.3903 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0696 1.1576 -0.0608 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4462 -0.0541 0.1394 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4272 1.3736 0.0388 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3677 0.4294 0.3449 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.3415 0.2485 -0.6406 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1118 1.3694 -0.8431 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.1959 0.9795 -1.8557 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8001 1.8615 0.4141 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.7203 2.1307 1.4381 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0235 0.7888 1.6794 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0047 -0.1386 1.9547 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1882 2.6892 2.6002 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5159 3.0074 0.0964 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1649 -2.9978 0.3938 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3729 -3.5543 0.1005 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6982 -4.8702 0.4158 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7924 -5.6690 1.0454 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5668 -5.1484 1.3561 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2606 -3.8516 1.0404 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0882 -6.9958 1.3761 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4118 3.9396 -1.6421 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7131 3.8253 -3.4042 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0967 3.5451 -2.2258 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6244 -0.5302 -1.1861 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9955 -0.1817 -1.9563 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0301 -0.6037 1.9216 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4260 -2.2793 0.7924 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2960 -2.0314 -0.6063 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1483 -0.1355 1.6806 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4857 1.0887 -0.4710 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9481 1.0716 2.3745 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2448 3.8758 -0.1565 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6983 3.1842 -0.5491 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0155 -0.9409 0.3975 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9147 -0.5623 0.4978 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5649 2.2140 -1.3058 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7599 1.8426 -2.2086 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8628 0.2321 -1.3632 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6850 0.4253 -2.6877 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4617 1.0678 0.8025 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9509 2.7738 0.9248 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2334 0.8511 2.4257 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7230 0.2508 2.5229 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8474 3.6290 2.6572 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4034 3.3067 -0.8272 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1106 -2.9764 -0.4242 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6730 -5.2446 0.1551 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1813 -5.7482 1.8555 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7089 -3.4453 1.2891 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6399 -7.7611 0.8885 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 1 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 10 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 18 21 1 0 21 22 1 0 21 23 2 0 23 24 1 0 24 25 2 0 24 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 29 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 32 35 1 0 31 36 1 0 15 37 1 0 37 38 2 0 38 39 1 0 39 40 2 0 40 41 1 0 41 42 2 0 40 43 1 0 11 6 1 0 19 14 1 0 33 27 1 0 42 37 1 0 25 17 1 0 1 44 1 0 1 45 1 0 1 46 1 0 5 47 1 0 5 48 1 0 7 49 1 0 8 50 1 0 8 51 1 0 10 52 1 1 11 53 1 6 12 54 1 0 22 55 1 0 23 56 1 0 25 57 1 0 27 58 1 1 29 59 1 6 30 60 1 0 30 61 1 0 30 62 1 0 31 63 1 1 32 64 1 6 33 65 1 1 34 66 1 0 35 67 1 0 36 68 1 0 38 69 1 0 39 70 1 0 41 71 1 0 42 72 1 0 43 73 1 0 M END

Standard InCHIKey	XOUMRQRJVFZBHB-BEAAOXLFSA-N
Standard InCHI	InChI=1S/C28H30O15/c1-11-19(32)21(34)22(35)26(40-11)41-15-7-16(31)18-17(8-15)42-23(13-3-5-14(30)6-4-13)24(20(18)33)43-27-25(36)28(37,10-39-27)9-38-12(2)29/h3-8,11,19,21-22,25-27,30-32,34-37H,9-10H2,1-2H3/t11-,19-,21+,22+,25+,26-,27+,28-/m0/s1
SMILES	CC(=O)OC[C@]1(O)CO[C@@H]([C@H]1O)Oc1c(oc2c(c1=O)c(O)cc(c2)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)c1ccc(cc1)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	606.16	Volume:	558.187 ? Van der Waals volume.
Dense:	1.086	LogP:	1.139 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.422 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.409 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	30.0
TPSA:	235.04 ? Topological Polar Surface Area.	H-Bond Acceptor:	15.0
H-Bond Donor:	7.0	Rings:	5.0
Heavy Atoms:	15.0

MedChem Properties

QED Drug-Likeness Score:	0.167	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.78	Fsp³:	0.429
MCE-18:	120.75 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.603	Fluc inhibitor:	0.304 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.833 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.624 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.033	Promiscuous compounds:	0.436

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.19	MDCK Permeability:	-5.159
Pgp-inhibitor:	0.001	Pgp-substrate:	0.951
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):	0.036
20% Bioavailability (F20%):	0.175	30% Bioavailability (F30%):	0.922
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.209
Plasma Protein Binding (PPB):	84.085%	Volume Distribution (VD):	-0.026
Fu:	16.686% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.988
OATP1B3 inhibitor:	0.989	BCRP inhibitor:	0.663
BSEP inhibitor:	0.432

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:	0.002
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.984
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.974
HLM stability:	0.342 ? 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):

1.444

Half-life (T1/2):

3.474

ADMET: Toxicity

hERG Blockers:	0.019	hERG Blockers (10um):	0.093
Human Hepatotoxicity (H-HT):	0.88	Drug-induced Liver Injury (DILI):	0.994
AMES Toxicity:	0.99	Rat Oral Acute Toxicity:	0.017
Maximum Recommended Daily Dose:	0.164	Skin Sensitization:	1.0
Carcinogencity:	0.374	Eye Corrosion:	0.0
Eye Irritation:	0.073	Respiratory Toxicity:	0.002
Drug-induced Neurotoxicity:	0.006	Ototoxicity:	0.886
Hematotoxicity:	0.103	Drug-induced Nephrotoxicity:	0.818
Genotoxicity:	0.997	RPMI-8226 Immunitoxicity:	0.256
A549 Cytotoxicity:	0.466	Hek293 Cytotoxicity:	0.638
BCF:	0.507 ? 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:	3.146 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.67 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.943 ? 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
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	flowers	n.a.	n.a.	PMID[16180811]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	branch	n.a.	PMID[22014228]
NPO27656	Lotus edulis	Species	Fabaceae	Eukaryota	n.a.	branch	n.a.	PMID[22014228]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22014228]
NPO27656	Lotus edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22014228]
NPO27656	Lotus edulis	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014228]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014228]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39355945]
NPO27656	Lotus edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Flower	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27656	Lotus edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23510	Vicia faba	Species	Fabaceae	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
IC50	6
Inhibition	4

Activity Type	# Activity
Individual protein	4
Cell line	3
Others	3

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT143	Individual protein	DNA topoisomerase I	Homo sapiens	IC50	=	150000.0	nM	PMID[12444694]
NPT1044	Individual protein	DNA topoisomerase II alpha	Homo sapiens	Inhibition	=	88.0	%	PMID[19258268]
NPT1044	Individual protein	DNA topoisomerase II alpha	Homo sapiens	Inhibition	=	22.0	%	PMID[19185486]
NPT1044	Individual protein	DNA topoisomerase II alpha	Homo sapiens	IC50	=	240000.0	nM	PMID[15104495]

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	=	350000.0	nM	PMID[12502331]
NPT165	Cell line	HeLa	Homo sapiens	IC50	=	350000.0	nM	PMID[12502331]
NPT65	Cell line	HepG2	Homo sapiens	IC50	=	410000.0	nM	PMID[17190456]
NPT2	Others	Unspecified	n.a.	IC50	=	120000.0	nM	PMID[24617951]
NPT2	Others	Unspecified	n.a.	Inhibition	=	44.0	%	PMID[3430167]
NPT2	Others	Unspecified	n.a.	Inhibition	=	99.0	%	PMID[26003344]

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 NPC72016 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	16601
0.1-0.2	30037
0.2-0.3	2440
0.3-0.4	346
0.4-0.5	281
0.5-0.6	106
0.6-0.7	21
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8353	Intermediate Similarity	NPC150164
0.8	Intermediate Similarity	NPC249281
0.7976	Intermediate Similarity	NPC276377
0.759	Intermediate Similarity	NPC46420
0.7442	Intermediate Similarity	NPC116458
0.7442	Intermediate Similarity	NPC246943
0.7253	Intermediate Similarity	NPC186816
0.686	Remote Similarity	NPC297987
0.6782	Remote Similarity	NPC271692
0.6667	Remote Similarity	NPC605784
0.6629	Remote Similarity	NPC611303
0.6495	Remote Similarity	NPC32641
0.6495	Remote Similarity	NPC256188
0.6495	Remote Similarity	NPC35119
0.6458	Remote Similarity	NPC64425
0.6437	Remote Similarity	NPC111929
0.6437	Remote Similarity	NPC320283
0.6437	Remote Similarity	NPC41121
0.6292	Remote Similarity	NPC158674
0.6277	Remote Similarity	NPC251417
0.6275	Remote Similarity	NPC121703
0.625	Remote Similarity	NPC331652
0.618	Remote Similarity	NPC289667
0.618	Remote Similarity	NPC108831
0.618	Remote Similarity	NPC182634
0.6162	Remote Similarity	NPC606657
0.6111	Remote Similarity	NPC136042
0.6095	Remote Similarity	NPC25523
0.5941	Remote Similarity	NPC142142
0.5824	Remote Similarity	NPC127546
0.5824	Remote Similarity	NPC57625
0.5824	Remote Similarity	NPC19709
0.5824	Remote Similarity	NPC173637
0.5824	Remote Similarity	NPC317489
0.5824	Remote Similarity	NPC238376
0.5824	Remote Similarity	NPC223424
0.5824	Remote Similarity	NPC600591
0.5816	Remote Similarity	NPC173582
0.5816	Remote Similarity	NPC265885
0.5816	Remote Similarity	NPC181465
0.5816	Remote Similarity	NPC215710
0.5816	Remote Similarity	NPC473438
0.5816	Remote Similarity	NPC253788
0.58	Remote Similarity	NPC240306
0.5714	Remote Similarity	NPC14187
0.5699	Remote Similarity	NPC84362
0.5699	Remote Similarity	NPC27640
0.5664	Remote Similarity	NPC209550
0.5657	Remote Similarity	NPC44931
0.5638	Remote Similarity	NPC59534
0.551	Remote Similarity	NPC116864
0.551	Remote Similarity	NPC244776
0.551	Remote Similarity	NPC265115
0.5505	Remote Similarity	NPC480441
0.5505	Remote Similarity	NPC164704
0.5484	Remote Similarity	NPC77672
0.5484	Remote Similarity	NPC133671
0.5484	Remote Similarity	NPC135391
0.5484	Remote Similarity	NPC78263
0.5484	Remote Similarity	NPC250069
0.5484	Remote Similarity	NPC348541
0.5481	Remote Similarity	NPC486577
0.5474	Remote Similarity	NPC27942
0.5464	Remote Similarity	NPC223747
0.5455	Remote Similarity	NPC277532
0.5446	Remote Similarity	NPC65563
0.5446	Remote Similarity	NPC470949
0.5437	Remote Similarity	NPC483414
0.5437	Remote Similarity	NPC483415
0.5417	Remote Similarity	NPC159579
0.5417	Remote Similarity	NPC219904
0.5408	Remote Similarity	NPC66087
0.5408	Remote Similarity	NPC190003
0.54	Remote Similarity	NPC471079
0.5392	Remote Similarity	NPC473571
0.5392	Remote Similarity	NPC110941
0.5391	Remote Similarity	NPC138990
0.5385	Remote Similarity	NPC483416
0.5385	Remote Similarity	NPC54802
0.5385	Remote Similarity	NPC197304
0.5376	Remote Similarity	NPC473043
0.5376	Remote Similarity	NPC135599
0.5376	Remote Similarity	NPC73855
0.5376	Remote Similarity	NPC113968
0.5376	Remote Similarity	NPC328940
0.5376	Remote Similarity	NPC277174
0.5376	Remote Similarity	NPC606877
0.5368	Remote Similarity	NPC305811
0.5368	Remote Similarity	NPC24043
0.5347	Remote Similarity	NPC67105
0.5345	Remote Similarity	NPC175429
0.534	Remote Similarity	NPC64051
0.5319	Remote Similarity	NPC39360
0.5319	Remote Similarity	NPC29763
0.5319	Remote Similarity	NPC210003
0.5304	Remote Similarity	NPC470720
0.5294	Remote Similarity	NPC203259
0.5294	Remote Similarity	NPC33054
0.5294	Remote Similarity	NPC210073
0.5294	Remote Similarity	NPC176740
0.5294	Remote Similarity	NPC471725
0.5294	Remote Similarity	NPC134532
0.5294	Remote Similarity	NPC602582
0.5288	Remote Similarity	NPC245452
0.5283	Remote Similarity	NPC470447
0.5268	Remote Similarity	NPC470716
0.5263	Remote Similarity	NPC265530
0.5263	Remote Similarity	NPC323593
0.5263	Remote Similarity	NPC203500
0.5258	Remote Similarity	NPC129217
0.5243	Remote Similarity	NPC129264
0.5234	Remote Similarity	NPC101636
0.5234	Remote Similarity	NPC298171
0.5225	Remote Similarity	NPC470715
0.5217	Remote Similarity	NPC470717
0.5208	Remote Similarity	NPC349108
0.5192	Remote Similarity	NPC153755
0.5161	Remote Similarity	NPC288084
0.5158	Remote Similarity	NPC476405
0.5155	Remote Similarity	NPC216496
0.5143	Remote Similarity	NPC470443
0.514	Remote Similarity	NPC85751
0.514	Remote Similarity	NPC19240
0.5104	Remote Similarity	NPC64305
0.5102	Remote Similarity	NPC175107
0.51	Remote Similarity	NPC476215
0.51	Remote Similarity	NPC355481
0.5098	Remote Similarity	NPC480466
0.5094	Remote Similarity	NPC270448
0.5053	Remote Similarity	NPC160515
0.5052	Remote Similarity	NPC488080
0.5052	Remote Similarity	NPC169977
0.5047	Remote Similarity	NPC270675
0.5047	Remote Similarity	NPC195685

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC72016 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4843
0.1-0.2	4252
0.2-0.3	47
0.3-0.4	3
0.4-0.5	2
0.5-0.6	3
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
0.5882	Remote Similarity	NPD7251	Phase 2
0.5514	Remote Similarity	NPD7808	Phase 3
0.5294	Remote Similarity	NPD6797	Phase 2

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