NPASS Compound

Structure

CID13879 OpenBabel06191715342D 21 24 0 0 0 0 0 0 0 0999 V2000 4.1728 1.4447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3387 1.9266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5034 1.4461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3383 -0.0007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6689 0.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1726 0.4809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5036 0.4822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5039 1.4451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6686 1.9278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5037 0.4812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8341 0.4819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8350 1.4454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8339 1.4457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0004 1.9273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8348 0.4815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0385 -0.0193 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3789 -0.0229 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6684 2.9385 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 2.9273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6694 -0.0003 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 1 6 1 0 0 0 0 2 8 1 0 0 0 0 3 7 2 0 0 0 0 3 9 1 0 0 0 0 4 6 2 0 0 0 0 4 10 1 0 0 0 0 5 7 1 0 0 0 0 5 11 2 0 0 0 0 6 16 1 0 0 0 0 7 17 1 0 0 0 0 8 10 2 0 0 0 0 8 12 1 0 0 0 0 9 13 2 0 0 0 0 9 18 1 0 0 0 0 10 20 1 0 0 0 0 11 13 1 0 0 0 0 11 21 1 0 0 0 0 12 14 1 0 0 0 0 12 15 2 0 0 0 0 13 14 1 0 0 0 0 14 19 2 0 0 0 0 15 20 1 0 0 0 0 15 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	520.3
Volume:	541.61
LogP:	4.605
LogD:	3.49
LogS:	-5.072
# Rotatable Bonds:	4
TPSA:	103.68
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.456
Synthetic Accessibility Score:	6.021
Fsp3:	0.69
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.678
MDCK Permeability:	5.053511631558649e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.658
Human Intestinal Absorption (HIA):	0.94
20% Bioavailability (F20%):	0.111
30% Bioavailability (F30%):	0.954

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.013
Plasma Protein Binding (PPB):	88.35957336425781%
Volume Distribution (VD):	1.756
Pgp-substrate:	2.076349973678589%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.78
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.793
CYP2C9-inhibitor:	0.009
CYP2C9-substrate:	0.017
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.148
CYP3A4-inhibitor:	0.144
CYP3A4-substrate:	0.446

ADMET: Excretion

Clearance (CL):	6.468
Half-life (T1/2):	0.031

ADMET: Toxicity

hERG Blockers:	0.385
Human Hepatotoxicity (H-HT):	0.885
Drug-inuced Liver Injury (DILI):	0.919
AMES Toxicity:	0.208
Rat Oral Acute Toxicity:	0.386
Maximum Recommended Daily Dose:	0.057
Skin Sensitization:	0.155
Carcinogencity:	0.023
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.955

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC13879

Natural Product ID:	NPC13879
*Common Name:**	1,3,8-Trihydroxy-[1]Benzofuro[2,3-B]Chromen-11-One
IUPAC Name:	1,3,8-trihydroxy-[1]benzofuro[2,3-b]chromen-11-one
Synonyms:
Standard InCHIKey:	BBBAWACESCACAP-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C15H8O6/c16-6-1-2-8-10(4-6)20-15-12(8)14(19)13-9(18)3-7(17)5-11(13)21-15/h1-5,16-18H
SMILES:	Oc1ccc2c(c1)oc1c2c(=O)c2c(o1)cc(cc2O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL312186
PubChem CID:	5324349
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0002901] Isoflav-2-enes [CHEMONTID:0000494] Isoflavones

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	root	n.a.	PMID[11374966]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[12964155]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16038550]
NPO11789	Swertia decussata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16286309]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17583950]
NPO733	Pseudoceratina arabica	Species	Pseudoceratinidae	Eukaryota	n.a.	Red Sea	n.a.	PMID[18598078]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18855446]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19191560]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20455578]
NPO12644	Lunularia cruciata	Species	Lunulariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21625478]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21775156]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23286284]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23377931]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24108414]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25620156]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27569393]
NPO4734	Syzygium nervosum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27797185]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29185738]
NPO16444	Apios americana	Species	Fabaceae	Eukaryota	Tubers	n.a.	n.a.	PMID[29932657]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30351923]
NPO12644	Lunularia cruciata	Species	Lunulariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30848895]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	root	n.a.	PMID[3655791]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	roots	n.a.	n.a.	PMID[9834151]
NPO24178	Citrus rugulosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26606	Macadamia ternifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7001	Berberis floribunda	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7319	Jamesoniella colorata	Species	Jungermanniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9452	Pulsatilla campanella	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8701	Bonamia spectabilis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24178	Citrus rugulosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7001	Berberis floribunda	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26606	Macadamia ternifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3311	Diplacus longiflorus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12864	Trogoderma granarium	Species	Dermestidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11534	Astragalus spinosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11910	Peltogyne pubescens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3658	Achillea pseudopectinata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO733	Pseudoceratina arabica	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12644	Lunularia cruciata	Species	Lunulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2280	Streptomyces griseochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO11223	Pleurotus japonicus	Species	Pleurotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23899	Rosulabryum capillare	Species	Bryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18447	Papaver tatricum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12169	Ranunculus peltatus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3292	Desmodium styracifolium	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16444	Apios americana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6572	Dunalia solanacea	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7319	Jamesoniella colorata	Species	Jungermanniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4910	Lepidosperma ustulatum	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8701	Bonamia spectabilis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7001	Berberis floribunda	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2565	Aglaia australiensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8006	Berlinia tomentosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9640	Dinophysis fortii	Species	Dinophysiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8398	Cymodocea nodosa	Species	Cymodoceaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12284	Hydrangea serrata	Species	Hydrangeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15439	Iyengaria stellata	Species	Scytosiphonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24178	Citrus rugulosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5743	Salvia miltiorrhiza	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4734	Syzygium nervosum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7627	Fumaria micrantha	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7949	Pterodon emarginatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9009	Atuna racemosa	Species	Chrysobalanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9226	Astragalus pycnanthus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11789	Swertia decussata	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10546	Allagopappus viscosissimus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26606	Macadamia ternifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9452	Pulsatilla campanella	Species	Ranunculaceae	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	NP ID	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
EC50	2
IC50	5
Others	3

Activity Type	# Activity
Cell Line	1
Individual Protein	7
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT248	Individual Protein	Estrogen receptor beta	Homo sapiens	IC50	=	1.7	nM	PMID[451023]
NPT108	Individual Protein	Estrogen receptor alpha	Homo sapiens	IC50	=	28.0	nM	PMID[451023]
NPT248	Individual Protein	Estrogen receptor beta	Homo sapiens	Fold selectivity	=	16.0	n.a.	PMID[451023]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	>	1000.0	nM	PMID[451024]
NPT1588	Individual Protein	Estradiol 17-beta-dehydrogenase 2	Homo sapiens	IC50	=	1520.0	nM	PMID[451025]
NPT1587	Individual Protein	Estradiol 17-beta-dehydrogenase 1	Homo sapiens	IC50	=	49.0	nM	PMID[451025]
NPT108	Individual Protein	Estrogen receptor alpha	Homo sapiens	EC50	=	21.4	nM	PMID[451025]
NPT155	Individual Protein	Aryl hydrocarbon receptor	Homo sapiens	EC50	=	1340.0	nM	PMID[451025]
NPT2	Others	Unspecified		Selectivity Index	=	0.03	n.a.	PMID[451025]
NPT2	Others	Unspecified		Ratio IC50	=	30.0	n.a.	PMID[451025]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC13879 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	491
0.1-0.2	2168
0.2-0.3	4832
0.3-0.4	10821
0.4-0.5	7083
0.5-0.6	4502
0.6-0.7	5845
0.7-0.8	4913
0.8-0.85	1646
0.85-0.9	375
0.9-0.95	19
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9797	High Similarity	NPC41326
0.9477	High Similarity	NPC244750
0.9427	High Similarity	NPC320789
0.9416	High Similarity	NPC260296
0.9416	High Similarity	NPC115432
0.9236	High Similarity	NPC155640
0.9067	High Similarity	NPC155144
0.9026	High Similarity	NPC67654
0.8968	High Similarity	NPC213608
0.8968	High Similarity	NPC1477
0.8961	High Similarity	NPC156244
0.8951	High Similarity	NPC120220
0.8944	High Similarity	NPC86477
0.894	High Similarity	NPC230943
0.8938	High Similarity	NPC29411
0.8933	High Similarity	NPC53192
0.8903	High Similarity	NPC5871
0.8896	High Similarity	NPC470107
0.8896	High Similarity	NPC472584
0.8874	High Similarity	NPC302181
0.8854	High Similarity	NPC247677
0.8854	High Similarity	NPC160015
0.8841	High Similarity	NPC261471
0.8839	High Similarity	NPC115324
0.8839	High Similarity	NPC23668
0.8839	High Similarity	NPC193976
0.8834	High Similarity	NPC218533
0.8834	High Similarity	NPC78830
0.8831	High Similarity	NPC226644
0.8831	High Similarity	NPC37226
0.8824	High Similarity	NPC17816
0.882	High Similarity	NPC329215
0.882	High Similarity	NPC259007
0.882	High Similarity	NPC204088
0.8816	High Similarity	NPC98926
0.8816	High Similarity	NPC131766
0.8812	High Similarity	NPC143402
0.8808	High Similarity	NPC471520
0.8802	High Similarity	NPC97523
0.8797	High Similarity	NPC65504
0.8797	High Similarity	NPC296957
0.8797	High Similarity	NPC260902
0.879	High Similarity	NPC99199
0.8782	High Similarity	NPC207624
0.8782	High Similarity	NPC142308
0.8774	High Similarity	NPC78335
0.8774	High Similarity	NPC230713
0.8774	High Similarity	NPC155882
0.8774	High Similarity	NPC167576
0.8766	High Similarity	NPC135325
0.8765	High Similarity	NPC323137
0.8758	High Similarity	NPC38591
0.8758	High Similarity	NPC210826
0.875	High Similarity	NPC225884
0.8742	High Similarity	NPC472877
0.8742	High Similarity	NPC310128
0.8742	High Similarity	NPC40583
0.8742	High Similarity	NPC476349
0.8742	High Similarity	NPC476350
0.8734	High Similarity	NPC137100
0.8733	High Similarity	NPC254994
0.8726	High Similarity	NPC472462
0.8726	High Similarity	NPC235333
0.8726	High Similarity	NPC72370
0.8718	High Similarity	NPC58668
0.8718	High Similarity	NPC170169
0.8718	High Similarity	NPC106372
0.8716	High Similarity	NPC9985
0.8716	High Similarity	NPC239495
0.871	High Similarity	NPC37208
0.871	High Similarity	NPC221868
0.871	High Similarity	NPC178202
0.8701	High Similarity	NPC12148
0.8701	High Similarity	NPC130581
0.8693	High Similarity	NPC32470
0.8693	High Similarity	NPC184649
0.8693	High Similarity	NPC303185
0.8684	High Similarity	NPC169479
0.8684	High Similarity	NPC159855
0.8684	High Similarity	NPC313036
0.8679	High Similarity	NPC268360
0.8679	High Similarity	NPC270044
0.8671	High Similarity	NPC213936
0.8671	High Similarity	NPC297531
0.8671	High Similarity	NPC148938
0.8654	High Similarity	NPC295036
0.8645	High Similarity	NPC272194
0.8642	High Similarity	NPC110257
0.8636	High Similarity	NPC267509
0.8636	High Similarity	NPC300267
0.8636	High Similarity	NPC299011
0.8636	High Similarity	NPC51641
0.8627	High Similarity	NPC113770
0.8623	High Similarity	NPC164384
0.8616	High Similarity	NPC211482
0.8616	High Similarity	NPC476652
0.8614	High Similarity	NPC59491
0.8614	High Similarity	NPC24748
0.8614	High Similarity	NPC37606
0.8609	High Similarity	NPC316480
0.8608	High Similarity	NPC122365
0.8599	High Similarity	NPC318424
0.8599	High Similarity	NPC116604
0.859	High Similarity	NPC296030
0.859	High Similarity	NPC39929
0.8571	High Similarity	NPC71210
0.8571	High Similarity	NPC311144
0.8571	High Similarity	NPC114147
0.8571	High Similarity	NPC300680
0.8563	High Similarity	NPC236327
0.8563	High Similarity	NPC290304
0.8562	High Similarity	NPC164110
0.8562	High Similarity	NPC269495
0.8562	High Similarity	NPC202981
0.8562	High Similarity	NPC212967
0.8562	High Similarity	NPC246647
0.8562	High Similarity	NPC96342
0.8553	High Similarity	NPC198490
0.8553	High Similarity	NPC474542
0.8545	High Similarity	NPC53252
0.8544	High Similarity	NPC263676
0.8544	High Similarity	NPC125300
0.8544	High Similarity	NPC253872
0.8543	High Similarity	NPC147686
0.8543	High Similarity	NPC472460
0.8543	High Similarity	NPC329225
0.8528	High Similarity	NPC109180
0.8528	High Similarity	NPC159508
0.8526	High Similarity	NPC39195
0.8523	High Similarity	NPC172262
0.8519	High Similarity	NPC162668
0.8519	High Similarity	NPC175513
0.8516	High Similarity	NPC154217
0.8512	High Similarity	NPC101991
0.85	High Similarity	NPC180924
0.85	High Similarity	NPC472461
0.8497	Intermediate Similarity	NPC254010
0.8491	Intermediate Similarity	NPC183874
0.8487	Intermediate Similarity	NPC261234
0.8487	Intermediate Similarity	NPC262635
0.8481	Intermediate Similarity	NPC148945
0.8481	Intermediate Similarity	NPC290671
0.8481	Intermediate Similarity	NPC204561
0.8481	Intermediate Similarity	NPC309512
0.8481	Intermediate Similarity	NPC316960
0.8481	Intermediate Similarity	NPC317715
0.8481	Intermediate Similarity	NPC78835
0.8477	Intermediate Similarity	NPC299379
0.8477	Intermediate Similarity	NPC243083
0.8477	Intermediate Similarity	NPC290291
0.8477	Intermediate Similarity	NPC107586
0.8477	Intermediate Similarity	NPC296490
0.8477	Intermediate Similarity	NPC275055
0.8477	Intermediate Similarity	NPC228661
0.8477	Intermediate Similarity	NPC103001
0.8477	Intermediate Similarity	NPC84585
0.8477	Intermediate Similarity	NPC32441
0.8477	Intermediate Similarity	NPC254841
0.8477	Intermediate Similarity	NPC287246
0.8477	Intermediate Similarity	NPC476480
0.8477	Intermediate Similarity	NPC79943
0.8477	Intermediate Similarity	NPC295261
0.8477	Intermediate Similarity	NPC12296
0.8477	Intermediate Similarity	NPC13768
0.8471	Intermediate Similarity	NPC88445
0.8471	Intermediate Similarity	NPC70764
0.8471	Intermediate Similarity	NPC317492
0.8466	Intermediate Similarity	NPC477239
0.8466	Intermediate Similarity	NPC310603
0.8466	Intermediate Similarity	NPC3448
0.8462	Intermediate Similarity	NPC308200
0.8462	Intermediate Similarity	NPC74539
0.8462	Intermediate Similarity	NPC304443
0.8462	Intermediate Similarity	NPC140120
0.8457	Intermediate Similarity	NPC169
0.8456	Intermediate Similarity	NPC213216
0.8456	Intermediate Similarity	NPC50898
0.8456	Intermediate Similarity	NPC78540
0.8456	Intermediate Similarity	NPC274121
0.8456	Intermediate Similarity	NPC57601
0.8452	Intermediate Similarity	NPC1886
0.8452	Intermediate Similarity	NPC316535
0.8452	Intermediate Similarity	NPC196137
0.8452	Intermediate Similarity	NPC246903
0.8447	Intermediate Similarity	NPC43638
0.8447	Intermediate Similarity	NPC161650
0.8443	Intermediate Similarity	NPC475964
0.8442	Intermediate Similarity	NPC226942
0.8442	Intermediate Similarity	NPC470636
0.8442	Intermediate Similarity	NPC36181
0.8442	Intermediate Similarity	NPC266725
0.8442	Intermediate Similarity	NPC144499
0.8442	Intermediate Similarity	NPC96791
0.8438	Intermediate Similarity	NPC469934
0.8434	Intermediate Similarity	NPC202470
0.8431	Intermediate Similarity	NPC182421
0.8431	Intermediate Similarity	NPC275734
0.8431	Intermediate Similarity	NPC220106
0.8431	Intermediate Similarity	NPC28337
0.8431	Intermediate Similarity	NPC69769

Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC13879 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	440
0.1-0.2	1005
0.2-0.3	1787
0.3-0.4	2700
0.4-0.5	1932
0.5-0.6	874
0.6-0.7	265
0.7-0.8	99
0.8-0.85	33
0.85-0.9	15
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9161	High Similarity	NPD3749	Approved
0.86	High Similarity	NPD2344	Approved
0.8543	High Similarity	NPD1549	Phase 2
0.8487	Intermediate Similarity	NPD1243	Approved
0.8477	Intermediate Similarity	NPD1550	Clinical (unspecified phase)
0.8477	Intermediate Similarity	NPD1552	Clinical (unspecified phase)
0.8462	Intermediate Similarity	NPD920	Approved
0.8452	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.8377	Intermediate Similarity	NPD2309	Approved
0.8344	Intermediate Similarity	NPD1510	Phase 2
0.8333	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.8323	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.8312	Intermediate Similarity	NPD3750	Approved
0.8284	Intermediate Similarity	NPD6559	Discontinued
0.825	Intermediate Similarity	NPD7411	Suspended
0.8217	Intermediate Similarity	NPD4378	Clinical (unspecified phase)
0.82	Intermediate Similarity	NPD1240	Approved
0.8155	Intermediate Similarity	NPD3818	Discontinued
0.8153	Intermediate Similarity	NPD1511	Approved
0.8148	Intermediate Similarity	NPD7819	Suspended
0.8144	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.8129	Intermediate Similarity	NPD2800	Approved
0.811	Intermediate Similarity	NPD7075	Discontinued
0.8101	Intermediate Similarity	NPD7410	Clinical (unspecified phase)
0.8092	Intermediate Similarity	NPD1607	Approved
0.8077	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.8057	Intermediate Similarity	NPD4287	Approved
0.8052	Intermediate Similarity	NPD1551	Phase 2
0.805	Intermediate Similarity	NPD1512	Approved
0.8049	Intermediate Similarity	NPD7768	Phase 2
0.8037	Intermediate Similarity	NPD1465	Phase 2
0.8037	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.7988	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.7987	Intermediate Similarity	NPD3748	Approved
0.7975	Intermediate Similarity	NPD1934	Approved
0.7973	Intermediate Similarity	NPD1203	Approved
0.7963	Intermediate Similarity	NPD4380	Phase 2
0.7949	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.7939	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.7935	Intermediate Similarity	NPD2796	Approved
0.7927	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.7925	Intermediate Similarity	NPD6799	Approved
0.7917	Intermediate Similarity	NPD6232	Discontinued
0.7901	Intermediate Similarity	NPD3226	Approved
0.7882	Intermediate Similarity	NPD7473	Discontinued
0.787	Intermediate Similarity	NPD3926	Phase 2
0.7853	Intermediate Similarity	NPD6599	Discontinued
0.7844	Intermediate Similarity	NPD919	Approved
0.7831	Intermediate Similarity	NPD3882	Suspended
0.7829	Intermediate Similarity	NPD2313	Discontinued
0.7818	Intermediate Similarity	NPD2801	Approved
0.7816	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.7791	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.7785	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7771	Intermediate Similarity	NPD2343	Clinical (unspecified phase)
0.7771	Intermediate Similarity	NPD2296	Approved
0.7764	Intermediate Similarity	NPD2534	Approved
0.7764	Intermediate Similarity	NPD2532	Approved
0.7764	Intermediate Similarity	NPD2533	Approved
0.7758	Intermediate Similarity	NPD6801	Discontinued
0.7756	Intermediate Similarity	NPD2799	Discontinued
0.7751	Intermediate Similarity	NPD6959	Discontinued
0.7746	Intermediate Similarity	NPD7074	Phase 3
0.7712	Intermediate Similarity	NPD3764	Approved
0.7692	Intermediate Similarity	NPD5494	Approved
0.7688	Intermediate Similarity	NPD5844	Phase 1
0.7688	Intermediate Similarity	NPD7054	Approved
0.7669	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.7665	Intermediate Similarity	NPD3817	Phase 2
0.7658	Intermediate Similarity	NPD2346	Discontinued
0.7651	Intermediate Similarity	NPD9717	Approved
0.7644	Intermediate Similarity	NPD7472	Approved
0.7616	Intermediate Similarity	NPD6166	Phase 2
0.7616	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.7616	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.76	Intermediate Similarity	NPD5953	Discontinued
0.76	Intermediate Similarity	NPD6797	Phase 2
0.7597	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7595	Intermediate Similarity	NPD2935	Discontinued
0.7561	Intermediate Similarity	NPD5403	Approved
0.756	Intermediate Similarity	NPD5402	Approved
0.7557	Intermediate Similarity	NPD7251	Discontinued
0.7547	Intermediate Similarity	NPD1471	Phase 3
0.7546	Intermediate Similarity	NPD5401	Approved
0.7544	Intermediate Similarity	NPD1247	Approved
0.7532	Intermediate Similarity	NPD1509	Clinical (unspecified phase)
0.7529	Intermediate Similarity	NPD3751	Discontinued
0.7529	Intermediate Similarity	NPD7893	Clinical (unspecified phase)
0.7514	Intermediate Similarity	NPD7808	Phase 3
0.75	Intermediate Similarity	NPD943	Approved
0.75	Intermediate Similarity	NPD6808	Phase 2
0.75	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.7486	Intermediate Similarity	NPD7286	Phase 2
0.7484	Intermediate Similarity	NPD3268	Approved
0.7467	Intermediate Similarity	NPD422	Phase 1
0.7452	Intermediate Similarity	NPD447	Suspended
0.7452	Intermediate Similarity	NPD1933	Approved
0.7451	Intermediate Similarity	NPD2798	Approved
0.7439	Intermediate Similarity	NPD7004	Clinical (unspecified phase)
0.7421	Intermediate Similarity	NPD4308	Phase 3
0.7407	Intermediate Similarity	NPD6398	Clinical (unspecified phase)
0.7407	Intermediate Similarity	NPD4628	Phase 3
0.7386	Intermediate Similarity	NPD2797	Approved
0.7378	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7377	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7374	Intermediate Similarity	NPD8313	Approved
0.7374	Intermediate Similarity	NPD8312	Approved
0.7355	Intermediate Similarity	NPD6832	Phase 2
0.7353	Intermediate Similarity	NPD4288	Approved
0.7351	Intermediate Similarity	NPD1610	Phase 2
0.7351	Intermediate Similarity	NPD1547	Clinical (unspecified phase)
0.7341	Intermediate Similarity	NPD7199	Phase 2
0.7337	Intermediate Similarity	NPD6280	Approved
0.7337	Intermediate Similarity	NPD6279	Approved
0.732	Intermediate Similarity	NPD3225	Approved
0.7318	Intermediate Similarity	NPD4419	Clinical (unspecified phase)
0.7303	Intermediate Similarity	NPD1608	Approved
0.7299	Intermediate Similarity	NPD5710	Approved
0.7299	Intermediate Similarity	NPD5711	Approved
0.7299	Intermediate Similarity	NPD7229	Phase 3
0.7273	Intermediate Similarity	NPD3267	Approved
0.7273	Intermediate Similarity	NPD1164	Approved
0.7273	Intermediate Similarity	NPD3266	Approved
0.7268	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7267	Intermediate Similarity	NPD6100	Approved
0.7267	Intermediate Similarity	NPD6099	Approved
0.7261	Intermediate Similarity	NPD1296	Phase 2
0.7261	Intermediate Similarity	NPD411	Approved
0.7257	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.7253	Intermediate Similarity	NPD8434	Phase 2
0.7244	Intermediate Similarity	NPD4908	Phase 1
0.7233	Intermediate Similarity	NPD230	Phase 1
0.7233	Intermediate Similarity	NPD1899	Clinical (unspecified phase)
0.7205	Intermediate Similarity	NPD7033	Discontinued
0.72	Intermediate Similarity	NPD3787	Discontinued
0.7193	Intermediate Similarity	NPD8455	Phase 2
0.7188	Intermediate Similarity	NPD6651	Approved
0.717	Intermediate Similarity	NPD4307	Phase 2
0.7169	Intermediate Similarity	NPD7390	Discontinued
0.7165	Intermediate Similarity	NPD8151	Discontinued
0.7161	Intermediate Similarity	NPD1470	Approved
0.716	Intermediate Similarity	NPD7458	Discontinued
0.716	Intermediate Similarity	NPD5406	Approved
0.716	Intermediate Similarity	NPD5405	Approved
0.716	Intermediate Similarity	NPD5408	Approved
0.716	Intermediate Similarity	NPD5808	Clinical (unspecified phase)
0.716	Intermediate Similarity	NPD5404	Approved
0.7152	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.7135	Intermediate Similarity	NPD37	Approved
0.7134	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7126	Intermediate Similarity	NPD6234	Discontinued
0.7115	Intermediate Similarity	NPD1019	Discontinued
0.711	Intermediate Similarity	NPD4967	Phase 2
0.711	Intermediate Similarity	NPD4966	Approved
0.711	Intermediate Similarity	NPD4965	Approved
0.7105	Intermediate Similarity	NPD17	Approved
0.7104	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7101	Intermediate Similarity	NPD1653	Approved
0.7099	Intermediate Similarity	NPD651	Clinical (unspecified phase)
0.7086	Intermediate Similarity	NPD1548	Phase 1
0.7086	Intermediate Similarity	NPD9545	Approved
0.7078	Intermediate Similarity	NPD1481	Phase 2
0.7076	Intermediate Similarity	NPD7615	Clinical (unspecified phase)
0.707	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7067	Intermediate Similarity	NPD9493	Approved
0.7013	Intermediate Similarity	NPD1535	Discovery
0.7005	Intermediate Similarity	NPD7782	Clinical (unspecified phase)
0.7005	Intermediate Similarity	NPD7783	Phase 2
0.6995	Remote Similarity	NPD7435	Discontinued
0.6988	Remote Similarity	NPD7003	Approved
0.6961	Remote Similarity	NPD1729	Discontinued
0.6957	Remote Similarity	NPD1613	Approved
0.6957	Remote Similarity	NPD1612	Clinical (unspecified phase)
0.6947	Remote Similarity	NPD8090	Clinical (unspecified phase)
0.6944	Remote Similarity	NPD7228	Approved
0.6932	Remote Similarity	NPD5537	Clinical (unspecified phase)
0.6931	Remote Similarity	NPD4363	Phase 3
0.6931	Remote Similarity	NPD4360	Phase 2
0.6928	Remote Similarity	NPD2654	Approved
0.6927	Remote Similarity	NPD6778	Approved
0.6927	Remote Similarity	NPD6779	Approved
0.6927	Remote Similarity	NPD6777	Approved
0.6927	Remote Similarity	NPD6776	Approved
0.6927	Remote Similarity	NPD6781	Approved
0.6927	Remote Similarity	NPD6782	Approved
0.6927	Remote Similarity	NPD6780	Approved
0.6915	Remote Similarity	NPD3269	Clinical (unspecified phase)
0.6914	Remote Similarity	NPD5124	Phase 1
0.6914	Remote Similarity	NPD5123	Clinical (unspecified phase)
0.6903	Remote Similarity	NPD1201	Approved
0.6897	Remote Similarity	NPD5761	Phase 2
0.6897	Remote Similarity	NPD5760	Phase 2
0.6895	Remote Similarity	NPD4361	Phase 2
0.6895	Remote Similarity	NPD4362	Clinical (unspecified phase)
0.6888	Remote Similarity	NPD7584	Approved
0.6885	Remote Similarity	NPD7685	Pre-registration
0.6879	Remote Similarity	NPD1876	Approved
0.6875	Remote Similarity	NPD6971	Discontinued
0.6875	Remote Similarity	NPD4625	Phase 3
0.6872	Remote Similarity	NPD7871	Phase 2

Bioactivity similarity: Similar Natural Products in NPASS

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