NPASS Compound

Structure

CID279930 OpenBabel06191716082D 24 27 0 0 0 0 0 0 0 0999 V2000 0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1369 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 1.1910 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 20 1 0 0 0 0 2 21 1 0 0 0 0 3 6 2 0 0 0 0 3 10 1 0 0 0 0 4 5 2 0 0 0 0 4 11 1 0 0 0 0 5 12 1 0 0 0 0 6 13 1 0 0 0 0 7 10 2 0 0 0 0 7 15 1 0 0 0 0 8 11 2 0 0 0 0 8 14 1 0 0 0 0 9 22 1 0 0 0 0 9 23 1 0 0 0 0 10 17 1 0 0 0 0 11 20 1 0 0 0 0 12 14 2 0 0 0 0 12 16 1 0 0 0 0 13 15 2 0 0 0 0 13 22 1 0 0 0 0 14 24 1 0 0 0 0 15 23 1 0 0 0 0 16 18 1 0 0 0 0 16 19 2 0 0 0 0 17 18 2 0 0 0 0 17 24 1 0 0 0 0 18 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	326.08
Volume:	317.308
LogP:	3.673
LogD:	3.261
LogS:	-5.273
# Rotatable Bonds:	3
TPSA:	67.13
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.736
Synthetic Accessibility Score:	2.195
Fsp3:	0.167
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.713
MDCK Permeability:	5.596262781182304e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.054
Plasma Protein Binding (PPB):	91.98209381103516%
Volume Distribution (VD):	0.766
Pgp-substrate:	7.375958442687988%

ADMET: Metabolism

CYP1A2-inhibitor:	0.973
CYP1A2-substrate:	0.806
CYP2C19-inhibitor:	0.962
CYP2C19-substrate:	0.176
CYP2C9-inhibitor:	0.836
CYP2C9-substrate:	0.933
CYP2D6-inhibitor:	0.923
CYP2D6-substrate:	0.936
CYP3A4-inhibitor:	0.957
CYP3A4-substrate:	0.24

ADMET: Excretion

Clearance (CL):	8.455
Half-life (T1/2):	0.235

ADMET: Toxicity

hERG Blockers:	0.058
Human Hepatotoxicity (H-HT):	0.248
Drug-inuced Liver Injury (DILI):	0.96
AMES Toxicity:	0.597
Rat Oral Acute Toxicity:	0.036
Maximum Recommended Daily Dose:	0.251
Skin Sensitization:	0.087
Carcinogencity:	0.928
Eye Corrosion:	0.003
Eye Irritation:	0.142
Respiratory Toxicity:	0.32

Download Data

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

Natural Product: NPC279930

Natural Product ID:	NPC279930
*Common Name:**	Demethoxykanugin
IUPAC Name:	2-(1,3-benzodioxol-5-yl)-3,7-dimethoxychromen-4-one
Synonyms:	Demethoxykanugin
Standard InCHIKey:	UBKPBGYXBIXFFC-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C18H14O6/c1-20-11-4-5-12-14(8-11)24-17(18(21-2)16(12)19)10-3-6-13-15(7-10)23-9-22-13/h3-8H,9H2,1-2H3
SMILES:	COc1c(oc2c(c1=O)ccc(c2)OC)c1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2205108
PubChem CID:	10381709
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002592] 7-O-methylated flavonoids

*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
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[10.1016/j.tet.2012.03.006]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/j.tet.2012.03.006]
NPO30165	Pongamia pinnata	Species	Fabaceae	Eukaryota	stem bark	Indonesia	1999-SEP	PMID[14510596]
NPO30165	Pongamia pinnata	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	PMID[14510596]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[16317898]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[17449162]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[19235686]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19666019]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[22707864]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23088673]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[2393954]
NPO30165	Pongamia pinnata	Species	Fabaceae	Eukaryota	dry stem	n.a.	n.a.	PMID[25466192]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[25594733]
NPO30165	Pongamia pinnata	Species	Fabaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29482940]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	seed	n.a.	PMID[7912074]
NPO17794	Streptomyces violaceusniger	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8557611]
NPO30165	Pongamia pinnata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18094	Euonymus atropurpureus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18094	Euonymus atropurpureus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28332	Lecidea tumida	Species	Lecideaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9416	Ostrea chilensis	Species	Ostreidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27972	Clitocybe phosphorea	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28007	Cakile maritima	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6223	Ceiba insignis	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6716	Amphimedon paraviridis	Species	Niphatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28157	Vriesea regina	Species	Bromeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4860	Coccinia grandis	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28299	Leucaena diversifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28245	Strychnos nux-vomica	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28142	Anthoceros agrestis	Species	Anthocerotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27863	Diospyros nigra	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17384	Festuca versuta	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17156	Neolitsea zeylanica	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17794	Streptomyces violaceusniger	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO18094	Euonymus atropurpureus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12255	Jasminum humile	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17852	Chilo suppressalis	Species	Crambidae	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
IC50	2
MIC	1

Activity Type	# Activity
Cell Line	1
Organism	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT34	Cell Line	BV-2	Mus musculus	IC50	=	14130.0	nM	PMID[558771]
NPT115	Organism	Mycobacterium tuberculosis H37Ra	Mycobacterium tuberculosis H37Ra	MIC	=	50.0	ug.mL-1	PMID[558770]
NPT2	Others	Unspecified		IC50	=	154500.0	nM	PMID[558772]

☑ 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 NPC279930 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	559
0.1-0.2	2165
0.2-0.3	5306
0.3-0.4	11272
0.4-0.5	6016
0.5-0.6	4121
0.6-0.7	5895
0.7-0.8	4655
0.8-0.85	1772
0.85-0.9	782
0.9-0.95	141
0.95-1	13

Similarity Score	Similarity Level	Natural Product ID
0.9932	High Similarity	NPC284353
0.9669	High Similarity	NPC269906
0.9603	High Similarity	NPC257914
0.9603	High Similarity	NPC104459
0.9603	High Similarity	NPC238405
0.9542	High Similarity	NPC302741
0.9539	High Similarity	NPC131557
0.953	High Similarity	NPC292460
0.953	High Similarity	NPC68882
0.9456	High Similarity	NPC117463
0.9456	High Similarity	NPC299923
0.9388	High Similarity	NPC310259
0.9338	High Similarity	NPC244371
0.932	High Similarity	NPC296575
0.9281	High Similarity	NPC310206
0.9272	High Similarity	NPC148497
0.9272	High Similarity	NPC153008
0.9252	High Similarity	NPC113089
0.9226	High Similarity	NPC34376
0.9221	High Similarity	NPC113055
0.9216	High Similarity	NPC155063
0.9211	High Similarity	NPC478213
0.9205	High Similarity	NPC474388
0.9205	High Similarity	NPC472535
0.9205	High Similarity	NPC474170
0.92	High Similarity	NPC69752
0.9189	High Similarity	NPC136278
0.9189	High Similarity	NPC224687
0.9184	High Similarity	NPC9966
0.9184	High Similarity	NPC70853
0.9177	High Similarity	NPC76482
0.9172	High Similarity	NPC187923
0.9156	High Similarity	NPC258644
0.9139	High Similarity	NPC259058
0.9139	High Similarity	NPC201547
0.9139	High Similarity	NPC177839
0.9133	High Similarity	NPC261548
0.9116	High Similarity	NPC29536
0.9103	High Similarity	NPC94155
0.9085	High Similarity	NPC57211
0.9079	High Similarity	NPC279061
0.9079	High Similarity	NPC236769
0.9073	High Similarity	NPC181250
0.9073	High Similarity	NPC159103
0.9068	High Similarity	NPC62640
0.9067	High Similarity	NPC205522
0.906	High Similarity	NPC471590
0.9045	High Similarity	NPC478199
0.9045	High Similarity	NPC18284
0.9045	High Similarity	NPC273021
0.9026	High Similarity	NPC34725
0.9026	High Similarity	NPC241774
0.9026	High Similarity	NPC276059
0.9026	High Similarity	NPC122623
0.9026	High Similarity	NPC478238
0.902	High Similarity	NPC55205
0.902	High Similarity	NPC279989
0.902	High Similarity	NPC104728
0.902	High Similarity	NPC35544
0.902	High Similarity	NPC304954
0.902	High Similarity	NPC82325
0.902	High Similarity	NPC52623
0.9013	High Similarity	NPC166753
0.9013	High Similarity	NPC50728
0.9	High Similarity	NPC40818
0.9	High Similarity	NPC215932
0.9	High Similarity	NPC110639
0.9	High Similarity	NPC14958
0.9	High Similarity	NPC106461
0.8994	High Similarity	NPC475214
0.8994	High Similarity	NPC113093
0.8994	High Similarity	NPC67037
0.8994	High Similarity	NPC254306
0.8994	High Similarity	NPC255615
0.8993	High Similarity	NPC293201
0.8974	High Similarity	NPC215375
0.8974	High Similarity	NPC62518
0.8968	High Similarity	NPC257277
0.8968	High Similarity	NPC265511
0.8961	High Similarity	NPC270620
0.8961	High Similarity	NPC179126
0.8961	High Similarity	NPC236223
0.8961	High Similarity	NPC78326
0.8954	High Similarity	NPC200740
0.8954	High Similarity	NPC54394
0.8954	High Similarity	NPC76376
0.8954	High Similarity	NPC260895
0.8954	High Similarity	NPC125062
0.8954	High Similarity	NPC252933
0.8944	High Similarity	NPC72249
0.8944	High Similarity	NPC206123
0.894	High Similarity	NPC85233
0.894	High Similarity	NPC12200
0.8938	High Similarity	NPC48640
0.8938	High Similarity	NPC149244
0.8931	High Similarity	NPC34531
0.8924	High Similarity	NPC125991
0.891	High Similarity	NPC167595
0.8903	High Similarity	NPC189960
0.8903	High Similarity	NPC32557
0.8903	High Similarity	NPC471746
0.8896	High Similarity	NPC134677
0.8896	High Similarity	NPC123886
0.8896	High Similarity	NPC301123
0.8889	High Similarity	NPC286342
0.8889	High Similarity	NPC245452
0.8889	High Similarity	NPC149127
0.8889	High Similarity	NPC188871
0.8889	High Similarity	NPC234152
0.8889	High Similarity	NPC219330
0.8882	High Similarity	NPC225434
0.8882	High Similarity	NPC195202
0.8882	High Similarity	NPC203050
0.8882	High Similarity	NPC223747
0.8882	High Similarity	NPC41853
0.8882	High Similarity	NPC476180
0.8882	High Similarity	NPC476771
0.8882	High Similarity	NPC63256
0.8882	High Similarity	NPC120099
0.8882	High Similarity	NPC219904
0.8882	High Similarity	NPC10304
0.8874	High Similarity	NPC231013
0.8874	High Similarity	NPC283002
0.8874	High Similarity	NPC302408
0.8867	High Similarity	NPC23955
0.8861	High Similarity	NPC295009
0.8861	High Similarity	NPC260640
0.8861	High Similarity	NPC182045
0.8861	High Similarity	NPC162668
0.8859	High Similarity	NPC185607
0.8854	High Similarity	NPC195832
0.8846	High Similarity	NPC245546
0.8846	High Similarity	NPC266960
0.8846	High Similarity	NPC178854
0.8846	High Similarity	NPC301897
0.8846	High Similarity	NPC43243
0.8844	High Similarity	NPC44573
0.8839	High Similarity	NPC86485
0.8839	High Similarity	NPC186507
0.8839	High Similarity	NPC476289
0.8839	High Similarity	NPC162351
0.8839	High Similarity	NPC246204
0.8839	High Similarity	NPC58382
0.8839	High Similarity	NPC473664
0.8836	High Similarity	NPC77955
0.8831	High Similarity	NPC28274
0.8831	High Similarity	NPC50403
0.8831	High Similarity	NPC133953
0.8831	High Similarity	NPC308451
0.8827	High Similarity	NPC475434
0.8824	High Similarity	NPC287101
0.8824	High Similarity	NPC183950
0.8824	High Similarity	NPC270465
0.8824	High Similarity	NPC52005
0.8824	High Similarity	NPC137062
0.8824	High Similarity	NPC223579
0.8824	High Similarity	NPC87125
0.882	High Similarity	NPC52550
0.882	High Similarity	NPC42892
0.882	High Similarity	NPC325555
0.882	High Similarity	NPC173637
0.882	High Similarity	NPC317489
0.882	High Similarity	NPC223424
0.882	High Similarity	NPC265530
0.882	High Similarity	NPC84362
0.882	High Similarity	NPC167479
0.882	High Similarity	NPC226304
0.882	High Similarity	NPC127546
0.8816	High Similarity	NPC470511
0.8816	High Similarity	NPC33265
0.8816	High Similarity	NPC62536
0.8808	High Similarity	NPC165512
0.8805	High Similarity	NPC414831
0.8805	High Similarity	NPC469575
0.8797	High Similarity	NPC110349
0.8797	High Similarity	NPC243509
0.8797	High Similarity	NPC285973
0.8797	High Similarity	NPC225624
0.879	High Similarity	NPC163524
0.879	High Similarity	NPC19097
0.879	High Similarity	NPC203891
0.879	High Similarity	NPC287979
0.879	High Similarity	NPC101830
0.879	High Similarity	NPC176665
0.879	High Similarity	NPC110070
0.879	High Similarity	NPC305663
0.8782	High Similarity	NPC18954
0.8782	High Similarity	NPC44079
0.8782	High Similarity	NPC201451
0.8782	High Similarity	NPC26227
0.8776	High Similarity	NPC72452
0.8776	High Similarity	NPC61546
0.8774	High Similarity	NPC39732
0.8774	High Similarity	NPC40033
0.8774	High Similarity	NPC60972
0.8773	High Similarity	NPC153755
0.8773	High Similarity	NPC476772
0.8773	High Similarity	NPC235575
0.8766	High Similarity	NPC306821
0.8766	High Similarity	NPC189270

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 NPC279930 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	462
0.1-0.2	1010
0.2-0.3	1923
0.3-0.4	2732
0.4-0.5	1719
0.5-0.6	853
0.6-0.7	315
0.7-0.8	95
0.8-0.85	28
0.85-0.9	12
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9026	High Similarity	NPD3817	Phase 2
0.8846	High Similarity	NPD3882	Suspended
0.882	High Similarity	NPD3818	Discontinued
0.8734	High Similarity	NPD919	Approved
0.8693	High Similarity	NPD6980	Clinical (unspecified phase)
0.8667	High Similarity	NPD7808	Phase 3
0.8659	High Similarity	NPD6797	Phase 2
0.8627	High Similarity	NPD1512	Approved
0.8625	High Similarity	NPD1247	Approved
0.8606	High Similarity	NPD7251	Discontinued
0.8599	High Similarity	NPD2801	Approved
0.8562	High Similarity	NPD5494	Approved
0.8554	High Similarity	NPD4338	Clinical (unspecified phase)
0.8537	High Similarity	NPD7054	Approved
0.8535	High Similarity	NPD1934	Approved
0.8497	Intermediate Similarity	NPD6799	Approved
0.8497	Intermediate Similarity	NPD1511	Approved
0.8485	Intermediate Similarity	NPD7472	Approved
0.8405	Intermediate Similarity	NPD3926	Phase 2
0.84	Intermediate Similarity	NPD2796	Approved
0.8373	Intermediate Similarity	NPD7074	Phase 3
0.8323	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.8323	Intermediate Similarity	NPD4378	Clinical (unspecified phase)
0.8255	Intermediate Similarity	NPD1933	Approved
0.825	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.825	Intermediate Similarity	NPD2393	Clinical (unspecified phase)
0.8242	Intermediate Similarity	NPD6166	Phase 2
0.8242	Intermediate Similarity	NPD6167	Clinical (unspecified phase)
0.8242	Intermediate Similarity	NPD6168	Clinical (unspecified phase)
0.8204	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.8187	Intermediate Similarity	NPD6801	Discontinued
0.8176	Intermediate Similarity	NPD6599	Discontinued
0.8098	Intermediate Similarity	NPD7075	Discontinued
0.8089	Intermediate Similarity	NPD5401	Approved
0.8086	Intermediate Similarity	NPD5402	Approved
0.8072	Intermediate Similarity	NPD7184	Clinical (unspecified phase)
0.8	Intermediate Similarity	NPD1243	Approved
0.7987	Intermediate Similarity	NPD920	Approved
0.7987	Intermediate Similarity	NPD5403	Approved
0.7974	Intermediate Similarity	NPD1510	Phase 2
0.7953	Intermediate Similarity	NPD6559	Discontinued
0.7935	Intermediate Similarity	NPD1549	Phase 2
0.7914	Intermediate Similarity	NPD7819	Suspended
0.7911	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7871	Intermediate Similarity	NPD1552	Clinical (unspecified phase)
0.7871	Intermediate Similarity	NPD1550	Clinical (unspecified phase)
0.7862	Intermediate Similarity	NPD642	Clinical (unspecified phase)
0.7857	Intermediate Similarity	NPD3748	Approved
0.7848	Intermediate Similarity	NPD643	Clinical (unspecified phase)
0.7844	Intermediate Similarity	NPD7199	Phase 2
0.784	Intermediate Similarity	NPD4380	Phase 2
0.7829	Intermediate Similarity	NPD1240	Approved
0.7818	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.7798	Intermediate Similarity	NPD6232	Discontinued
0.7765	Intermediate Similarity	NPD7473	Discontinued
0.775	Intermediate Similarity	NPD7410	Clinical (unspecified phase)
0.7727	Intermediate Similarity	NPD1607	Approved
0.7719	Intermediate Similarity	NPD3751	Discontinued
0.7707	Intermediate Similarity	NPD970	Clinical (unspecified phase)
0.7683	Intermediate Similarity	NPD7411	Suspended
0.7674	Intermediate Similarity	NPD5844	Phase 1
0.7662	Intermediate Similarity	NPD447	Suspended
0.761	Intermediate Similarity	NPD3750	Approved
0.761	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.759	Intermediate Similarity	NPD1465	Phase 2
0.7588	Intermediate Similarity	NPD3787	Discontinued
0.7586	Intermediate Similarity	NPD7993	Clinical (unspecified phase)
0.756	Intermediate Similarity	NPD3749	Approved
0.7548	Intermediate Similarity	NPD1899	Clinical (unspecified phase)
0.753	Intermediate Similarity	NPD37	Approved
0.75	Intermediate Similarity	NPD4966	Approved
0.75	Intermediate Similarity	NPD4967	Phase 2
0.75	Intermediate Similarity	NPD4965	Approved
0.75	Intermediate Similarity	NPD2403	Approved
0.7484	Intermediate Similarity	NPD943	Approved
0.7468	Intermediate Similarity	NPD1551	Phase 2
0.7468	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7451	Intermediate Similarity	NPD6832	Phase 2
0.744	Intermediate Similarity	NPD8443	Clinical (unspecified phase)
0.7438	Intermediate Similarity	NPD2800	Approved
0.7434	Intermediate Similarity	NPD2798	Approved
0.7421	Intermediate Similarity	NPD1471	Phase 3
0.7412	Intermediate Similarity	NPD6234	Discontinued
0.7399	Intermediate Similarity	NPD7784	Clinical (unspecified phase)
0.7394	Intermediate Similarity	NPD1653	Approved
0.7374	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7363	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7358	Intermediate Similarity	NPD2935	Discontinued
0.7355	Intermediate Similarity	NPD2313	Discontinued
0.7341	Intermediate Similarity	NPD5242	Approved
0.7333	Intermediate Similarity	NPD1547	Clinical (unspecified phase)
0.7329	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7329	Intermediate Similarity	NPD2654	Approved
0.7326	Intermediate Similarity	NPD6959	Discontinued
0.7325	Intermediate Similarity	NPD230	Phase 1
0.7317	Intermediate Similarity	NPD2534	Approved
0.7317	Intermediate Similarity	NPD2533	Approved
0.7317	Intermediate Similarity	NPD2532	Approved
0.7312	Intermediate Similarity	NPD2344	Approved
0.7299	Intermediate Similarity	NPD7852	Clinical (unspecified phase)
0.7296	Intermediate Similarity	NPD651	Clinical (unspecified phase)
0.7294	Intermediate Similarity	NPD7768	Phase 2
0.7262	Intermediate Similarity	NPD6385	Approved
0.7262	Intermediate Similarity	NPD6386	Approved
0.7247	Intermediate Similarity	NPD7685	Pre-registration
0.7246	Intermediate Similarity	NPD3226	Approved
0.7235	Intermediate Similarity	NPD5353	Approved
0.723	Intermediate Similarity	NPD5536	Phase 2
0.7226	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7219	Intermediate Similarity	NPD3705	Approved
0.7205	Intermediate Similarity	NPD2353	Approved
0.7205	Intermediate Similarity	NPD2346	Discontinued
0.7205	Intermediate Similarity	NPD2355	Clinical (unspecified phase)
0.7196	Intermediate Similarity	NPD5006	Approved
0.7196	Intermediate Similarity	NPD5005	Approved
0.7188	Intermediate Similarity	NPD2799	Discontinued
0.7178	Intermediate Similarity	NPD4628	Phase 3
0.7161	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7158	Intermediate Similarity	NPD8397	Clinical (unspecified phase)
0.7152	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7152	Intermediate Similarity	NPD1613	Approved
0.7152	Intermediate Similarity	NPD4307	Phase 2
0.7143	Intermediate Similarity	NPD3266	Approved
0.7143	Intermediate Similarity	NPD3267	Approved
0.7143	Intermediate Similarity	NPD1203	Approved
0.7134	Intermediate Similarity	NPD3887	Approved
0.7134	Intermediate Similarity	NPD2309	Approved
0.7134	Intermediate Similarity	NPD6190	Approved
0.7119	Intermediate Similarity	NPD7228	Approved
0.7119	Intermediate Similarity	NPD2163	Approved
0.7111	Intermediate Similarity	NPD4419	Clinical (unspecified phase)
0.7108	Intermediate Similarity	NPD3688	Clinical (unspecified phase)
0.7108	Intermediate Similarity	NPD3146	Approved
0.7097	Intermediate Similarity	NPD1019	Discontinued
0.7093	Intermediate Similarity	NPD5019	Clinical (unspecified phase)
0.709	Intermediate Similarity	NPD5457	Discontinued
0.7086	Intermediate Similarity	NPD17	Approved
0.7074	Intermediate Similarity	NPD4420	Approved
0.7059	Intermediate Similarity	NPD9717	Approved
0.7051	Intermediate Similarity	NPD3018	Phase 2
0.7049	Intermediate Similarity	NPD8434	Phase 2
0.7041	Intermediate Similarity	NPD7458	Discontinued
0.703	Intermediate Similarity	NPD2354	Approved
0.7025	Intermediate Similarity	NPD1296	Phase 2
0.7025	Intermediate Similarity	NPD6798	Discontinued
0.7021	Intermediate Similarity	NPD8090	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD6780	Approved
0.7	Intermediate Similarity	NPD5953	Discontinued
0.7	Intermediate Similarity	NPD6777	Approved
0.7	Intermediate Similarity	NPD6779	Approved
0.7	Intermediate Similarity	NPD7501	Clinical (unspecified phase)
0.7	Intermediate Similarity	NPD6778	Approved
0.7	Intermediate Similarity	NPD6782	Approved
0.7	Intermediate Similarity	NPD6776	Approved
0.7	Intermediate Similarity	NPD6355	Discontinued
0.7	Intermediate Similarity	NPD6781	Approved
0.6983	Remote Similarity	NPD7286	Phase 2
0.6981	Remote Similarity	NPD6233	Phase 2
0.6979	Remote Similarity	NPD7435	Discontinued
0.6978	Remote Similarity	NPD8313	Approved
0.6978	Remote Similarity	NPD8312	Approved
0.6975	Remote Similarity	NPD1509	Clinical (unspecified phase)
0.6975	Remote Similarity	NPD7033	Discontinued
0.6975	Remote Similarity	NPD4308	Phase 3
0.6964	Remote Similarity	NPD1940	Clinical (unspecified phase)
0.6962	Remote Similarity	NPD3027	Phase 3
0.6961	Remote Similarity	NPD7240	Approved
0.6959	Remote Similarity	NPD7584	Approved
0.6959	Remote Similarity	NPD1241	Discontinued
0.6948	Remote Similarity	NPD1608	Approved
0.6948	Remote Similarity	NPD2981	Phase 2
0.6948	Remote Similarity	NPD3972	Approved
0.6943	Remote Similarity	NPD9494	Approved
0.6936	Remote Similarity	NPD4288	Approved
0.6933	Remote Similarity	NPD6099	Approved
0.6933	Remote Similarity	NPD6100	Approved
0.6918	Remote Similarity	NPD3268	Approved
0.6918	Remote Similarity	NPD411	Approved
0.6914	Remote Similarity	NPD5537	Clinical (unspecified phase)
0.6903	Remote Similarity	NPD4379	Clinical (unspecified phase)
0.6903	Remote Similarity	NPD2982	Phase 2
0.6903	Remote Similarity	NPD2983	Phase 2
0.6901	Remote Similarity	NPD7028	Phase 2
0.6893	Remote Similarity	NPD7229	Phase 3
0.6891	Remote Similarity	NPD7696	Phase 3
0.6891	Remote Similarity	NPD7698	Approved
0.6891	Remote Similarity	NPD7697	Approved
0.6883	Remote Similarity	NPD422	Phase 1
0.6867	Remote Similarity	NPD6398	Clinical (unspecified phase)
0.6859	Remote Similarity	NPD1876	Approved
0.6859	Remote Similarity	NPD3225	Approved
0.6857	Remote Similarity	NPD6971	Discontinued
0.6856	Remote Similarity	NPD7870	Phase 2
0.6856	Remote Similarity	NPD7871	Phase 2
0.6852	Remote Similarity	NPD6651	Approved
0.6845	Remote Similarity	NPD4357	Discontinued
0.6842	Remote Similarity	NPD1548	Phase 1
0.6833	Remote Similarity	NPD7893	Clinical (unspecified phase)
0.6821	Remote Similarity	NPD6844	Discontinued
0.6821	Remote Similarity	NPD6279	Approved

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