NPASS Compound

Structure

CID103947 OpenBabel06191715452D 24 26 0 0 0 0 0 0 0 0999 V2000 6.1472 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0132 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2812 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0132 1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4152 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8793 1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.0600 0.8546 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.5600 -0.0115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7453 1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.3909 1.5977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5819 0.1965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6113 1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4773 1.1910 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 9.6113 2.6910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.6180 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 1 0 0 0 0 1 3 1 0 0 0 0 2 4 2 0 0 0 0 3 5 1 0 0 0 0 4 6 1 0 0 0 0 5 9 2 0 0 0 0 6 10 2 0 0 0 0 7 8 1 0 0 0 0 7 13 1 0 0 0 0 8 14 1 0 0 0 0 9 17 1 0 0 0 0 10 20 1 0 0 0 0 11 12 2 0 0 0 0 11 17 1 0 0 0 0 12 18 1 0 0 0 0 13 21 1 0 0 0 0 14 21 1 0 0 0 0 15 17 2 0 0 0 0 15 19 1 0 0 0 0 16 23 1 0 0 0 0 16 24 1 0 0 0 0 18 19 2 0 0 0 0 18 23 1 0 0 0 0 19 24 1 0 0 0 0 20 21 1 0 0 0 0 20 22 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	325.17
Volume:	347.719
LogP:	3.617
LogD:	3.374
LogS:	-4.067
# Rotatable Bonds:	7
TPSA:	38.77
# H-Bond Aceptor:	4
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.452
Synthetic Accessibility Score:	2.645
Fsp3:	0.35
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:	-4.842
MDCK Permeability:	2.5272374841733836e-05
Pgp-inhibitor:	0.993
Pgp-substrate:	0.019
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.121
30% Bioavailability (F30%):	0.338

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.261
Plasma Protein Binding (PPB):	97.37667083740234%
Volume Distribution (VD):	0.962
Pgp-substrate:	2.635343074798584%

ADMET: Metabolism

CYP1A2-inhibitor:	0.974
CYP1A2-substrate:	0.614
CYP2C19-inhibitor:	0.832
CYP2C19-substrate:	0.42
CYP2C9-inhibitor:	0.423
CYP2C9-substrate:	0.89
CYP2D6-inhibitor:	0.942
CYP2D6-substrate:	0.914
CYP3A4-inhibitor:	0.947
CYP3A4-substrate:	0.291

ADMET: Excretion

Clearance (CL):	10.1
Half-life (T1/2):	0.565

ADMET: Toxicity

hERG Blockers:	0.892
Human Hepatotoxicity (H-HT):	0.708
Drug-inuced Liver Injury (DILI):	0.126
AMES Toxicity:	0.124
Rat Oral Acute Toxicity:	0.096
Maximum Recommended Daily Dose:	0.333
Skin Sensitization:	0.975
Carcinogencity:	0.817
Eye Corrosion:	0.028
Eye Irritation:	0.137
Respiratory Toxicity:	0.974

Download Data

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

Natural Product: NPC103947

Natural Product ID:	NPC103947
*Common Name:**	9-(Benzo[D][1,3]Dioxol-5-Yl)-1-(Pyrrolidin-1-Yl)Nona-2,4,8-Trien-1-One
IUPAC Name:	(2E,4E,8E)-9-(1,3-benzodioxol-5-yl)-1-pyrrolidin-1-ylnona-2,4,8-trien-1-one
Synonyms:
Standard InCHIKey:	XWQSYLYFCJTIEL-BTLPPRQPSA-N
Standard InCHI:	InChI=1S/C20H23NO3/c22-20(21-13-7-8-14-21)10-6-4-2-1-3-5-9-17-11-12-18-19(15-17)24-16-23-18/h2,4-6,9-12,15H,1,3,7-8,13-14,16H2/b4-2+,9-5+,10-6+
SMILES:	O=C(N1CCCC1)/C=C/C=C/CC/C=C/c1ccc2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1669578
PubChem CID:	11964516
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000296] Benzodioxoles

*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
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	whole plants	Sendai, Miyagi Prefecture, Japan	2000-Sep	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17397219]
NPO30128	Piper boehmeriaefolium	Species	Piperaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[21158422]
NPO30128	Piper boehmeriaefolium	Species	Piperaceae	Eukaryota	whole plant	Luxi County, Yunnan Province, China	2008-OCT	PMID[21158422]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	aerial parts	Kego Nature Reserve, Hatinh Province, Vietnam	2008-DEC	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	stem	n.a.	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	inflorescence	n.a.	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	Kego Nature Reserve, Hatinh Province, Vietnam	2008-DEC	PMID[21973101]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	twig	n.a.	PMID[21973101]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22940450]
NPO4720	Aglaia perviridis	Species	Meliaceae	Eukaryota	leaves, twigs, and fruits	Nui Chua National Park (11 43' N; 109 08' E; 730 m alt.), Ninh Thuan Province, Vietnam	2010-Jan	PMID[23301897]
NPO4720	Aglaia perviridis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31621322]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30128	Piper boehmeriaefolium	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6614	Rubus pileatus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO61	Phoebe grandis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO992	Betula alnoides	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2846	Piper sarmentosum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5657	Oocystis polymorpha	Species	Oocystaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4720	Aglaia perviridis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1912	Acanthosyris paulo-alvinii	Species	Cervantesiaceae	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	9
MIC	1

Activity Type	# Activity
Cell Line	8
NON-MOLECULAR	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	13.74	ug.mL-1	PMID[501773]
NPT81	Cell Line	A549	Homo sapiens	IC50	>	40000.0	nM	PMID[501775]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	40000.0	nM	PMID[501775]
NPT133	Cell Line	ZR-75-1	Homo sapiens	IC50	>	40000.0	nM	PMID[501775]
NPT134	Cell Line	SK-BR-3	Homo sapiens	IC50	>	40000.0	nM	PMID[501775]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	>	40000.0	nM	PMID[501775]
NPT90	Cell Line	DU-145	Homo sapiens	IC50	>	40000.0	nM	PMID[501775]
NPT91	Cell Line	KB	Homo sapiens	IC50	>	40000.0	nM	PMID[501775]
NPT115	Organism	Mycobacterium tuberculosis H37Ra	Mycobacterium tuberculosis H37Ra	MIC	=	25.0	ug.mL-1	PMID[501774]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	>	40000.0	nM	PMID[501775]

☑ 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 NPC103947 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	229
0.1-0.2	1820
0.2-0.3	8478
0.3-0.4	10249
0.4-0.5	7341
0.5-0.6	11559
0.6-0.7	2682
0.7-0.8	295
0.8-0.85	12
0.85-0.9	4
0.9-0.95	16
0.95-1	12

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC159150
1.0	High Similarity	NPC193673
1.0	High Similarity	NPC328419
1.0	High Similarity	NPC94280
1.0	High Similarity	NPC45783
0.9921	High Similarity	NPC96406
0.9844	High Similarity	NPC145446
0.9844	High Similarity	NPC137172
0.9841	High Similarity	NPC217574
0.9767	High Similarity	NPC95366
0.9767	High Similarity	NPC248505
0.9531	High Similarity	NPC318862
0.9462	High Similarity	NPC196609
0.9462	High Similarity	NPC230698
0.9462	High Similarity	NPC73883
0.9462	High Similarity	NPC205178
0.9462	High Similarity	NPC136330
0.9462	High Similarity	NPC255817
0.9462	High Similarity	NPC277042
0.9462	High Similarity	NPC251454
0.9389	High Similarity	NPC99078
0.9385	High Similarity	NPC167096
0.9318	High Similarity	NPC220923
0.9318	High Similarity	NPC252107
0.9318	High Similarity	NPC470707
0.9173	High Similarity	NPC28641
0.9173	High Similarity	NPC194359
0.8881	High Similarity	NPC180647
0.8815	High Similarity	NPC469808
0.875	High Similarity	NPC225745
0.8643	High Similarity	NPC244338
0.8425	Intermediate Similarity	NPC270811
0.8425	Intermediate Similarity	NPC471073
0.8311	Intermediate Similarity	NPC169742
0.8286	Intermediate Similarity	NPC231572
0.8243	Intermediate Similarity	NPC470708
0.8231	Intermediate Similarity	NPC69670
0.8214	Intermediate Similarity	NPC214036
0.8214	Intermediate Similarity	NPC113236
0.814	Intermediate Similarity	NPC111225
0.8077	Intermediate Similarity	NPC199209
0.8077	Intermediate Similarity	NPC212643
0.8069	Intermediate Similarity	NPC469978
0.8045	Intermediate Similarity	NPC114845
0.8041	Intermediate Similarity	NPC223125
0.8015	Intermediate Similarity	NPC251466
0.7987	Intermediate Similarity	NPC474852
0.7985	Intermediate Similarity	NPC256167
0.7955	Intermediate Similarity	NPC57501
0.7941	Intermediate Similarity	NPC182147
0.7941	Intermediate Similarity	NPC71105
0.7941	Intermediate Similarity	NPC152186
0.7941	Intermediate Similarity	NPC207541
0.7941	Intermediate Similarity	NPC170583
0.7941	Intermediate Similarity	NPC246133
0.7935	Intermediate Similarity	NPC231198
0.7933	Intermediate Similarity	NPC223124
0.7899	Intermediate Similarity	NPC469977
0.7887	Intermediate Similarity	NPC416184
0.7883	Intermediate Similarity	NPC156944
0.7874	Intermediate Similarity	NPC127326
0.7872	Intermediate Similarity	NPC473463
0.7868	Intermediate Similarity	NPC300955
0.7857	Intermediate Similarity	NPC118419
0.7852	Intermediate Similarity	NPC470088
0.7842	Intermediate Similarity	NPC470706
0.7826	Intermediate Similarity	NPC41331
0.7826	Intermediate Similarity	NPC157740
0.7826	Intermediate Similarity	NPC291449
0.7826	Intermediate Similarity	NPC99798
0.7826	Intermediate Similarity	NPC191302
0.7812	Intermediate Similarity	NPC31279
0.777	Intermediate Similarity	NPC147247
0.777	Intermediate Similarity	NPC246974
0.7762	Intermediate Similarity	NPC7018
0.7754	Intermediate Similarity	NPC218323
0.7746	Intermediate Similarity	NPC282477
0.7746	Intermediate Similarity	NPC284855
0.7698	Intermediate Similarity	NPC64948
0.7698	Intermediate Similarity	NPC172403
0.7692	Intermediate Similarity	NPC11147
0.7647	Intermediate Similarity	NPC301641
0.7647	Intermediate Similarity	NPC80241
0.7647	Intermediate Similarity	NPC193484
0.7597	Intermediate Similarity	NPC78733
0.7597	Intermediate Similarity	NPC76079
0.7586	Intermediate Similarity	NPC193528
0.7564	Intermediate Similarity	NPC106786
0.7554	Intermediate Similarity	NPC85830
0.755	Intermediate Similarity	NPC475959
0.7538	Intermediate Similarity	NPC179309
0.7532	Intermediate Similarity	NPC59567
0.75	Intermediate Similarity	NPC344161
0.7481	Intermediate Similarity	NPC277460
0.7468	Intermediate Similarity	NPC210148
0.7468	Intermediate Similarity	NPC148898
0.7468	Intermediate Similarity	NPC233029
0.7467	Intermediate Similarity	NPC145304
0.7466	Intermediate Similarity	NPC230968
0.7466	Intermediate Similarity	NPC102260
0.7465	Intermediate Similarity	NPC476748
0.7464	Intermediate Similarity	NPC298486
0.7463	Intermediate Similarity	NPC268317
0.7453	Intermediate Similarity	NPC241055
0.7453	Intermediate Similarity	NPC86469
0.7448	Intermediate Similarity	NPC475828
0.7447	Intermediate Similarity	NPC286683
0.7444	Intermediate Similarity	NPC294941
0.744	Intermediate Similarity	NPC471650
0.7436	Intermediate Similarity	NPC31311
0.7436	Intermediate Similarity	NPC234392
0.7431	Intermediate Similarity	NPC266425
0.7429	Intermediate Similarity	NPC120066
0.7415	Intermediate Similarity	NPC166184
0.7413	Intermediate Similarity	NPC477694
0.7413	Intermediate Similarity	NPC477705
0.7407	Intermediate Similarity	NPC185738
0.7407	Intermediate Similarity	NPC33271
0.7407	Intermediate Similarity	NPC280001
0.7405	Intermediate Similarity	NPC97072
0.7405	Intermediate Similarity	NPC215829
0.7386	Intermediate Similarity	NPC469540
0.7386	Intermediate Similarity	NPC469539
0.7378	Intermediate Similarity	NPC308267
0.7376	Intermediate Similarity	NPC213711
0.7376	Intermediate Similarity	NPC40352
0.7365	Intermediate Similarity	NPC102760
0.7365	Intermediate Similarity	NPC178290
0.7361	Intermediate Similarity	NPC477706
0.7347	Intermediate Similarity	NPC254610
0.7343	Intermediate Similarity	NPC160193
0.7324	Intermediate Similarity	NPC177167
0.7324	Intermediate Similarity	NPC158737
0.7323	Intermediate Similarity	NPC310905
0.7323	Intermediate Similarity	NPC12714
0.7321	Intermediate Similarity	NPC83511
0.7319	Intermediate Similarity	NPC471877
0.7315	Intermediate Similarity	NPC278076
0.7315	Intermediate Similarity	NPC275150
0.7299	Intermediate Similarity	NPC119949
0.7299	Intermediate Similarity	NPC37858
0.7296	Intermediate Similarity	NPC165797
0.729	Intermediate Similarity	NPC119669
0.7286	Intermediate Similarity	NPC249788
0.7284	Intermediate Similarity	NPC57812
0.7284	Intermediate Similarity	NPC474324
0.7279	Intermediate Similarity	NPC120075
0.7279	Intermediate Similarity	NPC307682
0.7273	Intermediate Similarity	NPC57119
0.7273	Intermediate Similarity	NPC181905
0.7273	Intermediate Similarity	NPC165128
0.7273	Intermediate Similarity	NPC158471
0.7273	Intermediate Similarity	NPC211296
0.7273	Intermediate Similarity	NPC226862
0.7267	Intermediate Similarity	NPC138438
0.7267	Intermediate Similarity	NPC908
0.7267	Intermediate Similarity	NPC168409
0.7267	Intermediate Similarity	NPC306669
0.7261	Intermediate Similarity	NPC138487
0.7261	Intermediate Similarity	NPC216459
0.7261	Intermediate Similarity	NPC41178
0.7261	Intermediate Similarity	NPC93593
0.726	Intermediate Similarity	NPC205915
0.7256	Intermediate Similarity	NPC303581
0.7256	Intermediate Similarity	NPC67978
0.7248	Intermediate Similarity	NPC318575
0.7246	Intermediate Similarity	NPC222175
0.7239	Intermediate Similarity	NPC475845
0.7233	Intermediate Similarity	NPC329640
0.7233	Intermediate Similarity	NPC477080
0.7226	Intermediate Similarity	NPC164706
0.7226	Intermediate Similarity	NPC272471
0.7226	Intermediate Similarity	NPC124916
0.7226	Intermediate Similarity	NPC107588
0.7226	Intermediate Similarity	NPC137537
0.7226	Intermediate Similarity	NPC70744
0.7219	Intermediate Similarity	NPC116007
0.7218	Intermediate Similarity	NPC245552
0.7215	Intermediate Similarity	NPC146288
0.7214	Intermediate Similarity	NPC288238
0.7211	Intermediate Similarity	NPC110958
0.7211	Intermediate Similarity	NPC19890
0.7209	Intermediate Similarity	NPC292792
0.7208	Intermediate Similarity	NPC59907
0.7208	Intermediate Similarity	NPC37144
0.7205	Intermediate Similarity	NPC320104
0.7205	Intermediate Similarity	NPC218614
0.7197	Intermediate Similarity	NPC292003
0.7195	Intermediate Similarity	NPC474708
0.7194	Intermediate Similarity	NPC224814
0.7194	Intermediate Similarity	NPC204466
0.7194	Intermediate Similarity	NPC109083
0.7194	Intermediate Similarity	NPC189844
0.7194	Intermediate Similarity	NPC269843
0.7194	Intermediate Similarity	NPC60962
0.7194	Intermediate Similarity	NPC14007
0.7183	Intermediate Similarity	NPC17348
0.7179	Intermediate Similarity	NPC476579
0.7176	Intermediate Similarity	NPC258171
0.7172	Intermediate Similarity	NPC171550

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 NPC103947 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	170
0.1-0.2	742
0.2-0.3	1234
0.3-0.4	2529
0.4-0.5	2636
0.5-0.6	1398
0.6-0.7	400
0.7-0.8	39
0.8-0.85	1
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9462	High Similarity	NPD2492	Phase 1
0.8264	Intermediate Similarity	NPD5297	Approved
0.8	Intermediate Similarity	NPD5084	Clinical (unspecified phase)
0.773	Intermediate Similarity	NPD554	Clinical (unspecified phase)
0.7584	Intermediate Similarity	NPD6783	Clinical (unspecified phase)
0.7566	Intermediate Similarity	NPD4210	Discontinued
0.7518	Intermediate Similarity	NPD5752	Clinical (unspecified phase)
0.7516	Intermediate Similarity	NPD824	Approved
0.7468	Intermediate Similarity	NPD1337	Clinical (unspecified phase)
0.7465	Intermediate Similarity	NPD2669	Clinical (unspecified phase)
0.7426	Intermediate Similarity	NPD1357	Approved
0.7413	Intermediate Similarity	NPD5718	Phase 2
0.741	Intermediate Similarity	NPD7281	Phase 3
0.741	Intermediate Similarity	NPD7280	Phase 3
0.7407	Intermediate Similarity	NPD5536	Phase 2
0.7397	Intermediate Similarity	NPD743	Approved
0.7372	Intermediate Similarity	NPD2423	Clinical (unspecified phase)
0.7273	Intermediate Similarity	NPD3885	Approved
0.7273	Intermediate Similarity	NPD6662	Clinical (unspecified phase)
0.7267	Intermediate Similarity	NPD4237	Approved
0.7267	Intermediate Similarity	NPD4236	Phase 3
0.7266	Intermediate Similarity	NPD3705	Approved
0.7255	Intermediate Similarity	NPD3688	Clinical (unspecified phase)
0.7255	Intermediate Similarity	NPD3146	Approved
0.7211	Intermediate Similarity	NPD2653	Approved
0.7203	Intermediate Similarity	NPD2040	Clinical (unspecified phase)
0.72	Intermediate Similarity	NPD1372	Clinical (unspecified phase)
0.7171	Intermediate Similarity	NPD2219	Phase 1
0.7163	Intermediate Similarity	NPD1420	Approved
0.7163	Intermediate Similarity	NPD1421	Approved
0.7162	Intermediate Similarity	NPD6895	Approved
0.7162	Intermediate Similarity	NPD6896	Approved
0.7114	Intermediate Similarity	NPD6029	Clinical (unspecified phase)
0.7114	Intermediate Similarity	NPD6028	Clinical (unspecified phase)
0.7089	Intermediate Similarity	NPD7109	Clinical (unspecified phase)
0.7089	Intermediate Similarity	NPD6386	Approved
0.7089	Intermediate Similarity	NPD6873	Phase 2
0.7089	Intermediate Similarity	NPD6385	Approved
0.7089	Intermediate Similarity	NPD7110	Phase 1
0.7086	Intermediate Similarity	NPD4664	Clinical (unspecified phase)
0.7081	Intermediate Similarity	NPD5604	Discontinued
0.7078	Intermediate Similarity	NPD4357	Discontinued
0.7063	Intermediate Similarity	NPD5977	Approved
0.7063	Intermediate Similarity	NPD5978	Approved
0.7055	Intermediate Similarity	NPD3145	Approved
0.7055	Intermediate Similarity	NPD3144	Approved
0.7051	Intermediate Similarity	NPD1670	Discontinued
0.7047	Intermediate Similarity	NPD6111	Discontinued
0.7045	Intermediate Similarity	NPD1358	Approved
0.7042	Intermediate Similarity	NPD4379	Clinical (unspecified phase)
0.7025	Intermediate Similarity	NPD6875	Approved
0.7025	Intermediate Similarity	NPD6876	Approved
0.7012	Intermediate Similarity	NPD4166	Phase 2
0.7007	Intermediate Similarity	NPD2245	Discovery
0.7007	Intermediate Similarity	NPD2674	Phase 3
0.7	Intermediate Similarity	NPD2978	Approved
0.7	Intermediate Similarity	NPD2977	Approved
0.6993	Remote Similarity	NPD5481	Discontinued
0.6985	Remote Similarity	NPD5283	Phase 1
0.697	Remote Similarity	NPD3134	Approved
0.6937	Remote Similarity	NPD7945	Clinical (unspecified phase)
0.6908	Remote Similarity	NPD1375	Discontinued
0.6879	Remote Similarity	NPD2667	Approved
0.6879	Remote Similarity	NPD2668	Approved
0.6875	Remote Similarity	NPD2922	Phase 1
0.6867	Remote Similarity	NPD4579	Clinical (unspecified phase)
0.6859	Remote Similarity	NPD6143	Clinical (unspecified phase)
0.6857	Remote Similarity	NPD5525	Clinical (unspecified phase)
0.6846	Remote Similarity	NPD3140	Approved
0.6846	Remote Similarity	NPD3142	Approved
0.6842	Remote Similarity	NPD2161	Phase 2
0.6839	Remote Similarity	NPD3349	Phase 2
0.6839	Remote Similarity	NPD5241	Discontinued
0.6838	Remote Similarity	NPD228	Approved
0.6835	Remote Similarity	NPD3640	Phase 3
0.6835	Remote Similarity	NPD3639	Approved
0.6835	Remote Similarity	NPD3641	Approved
0.6833	Remote Similarity	NPD5457	Discontinued
0.6818	Remote Similarity	NPD4162	Approved
0.6818	Remote Similarity	NPD3060	Approved
0.6815	Remote Similarity	NPD4739	Approved
0.6815	Remote Similarity	NPD4584	Approved
0.6798	Remote Similarity	NPD5582	Discontinued
0.6797	Remote Similarity	NPD3656	Approved
0.6795	Remote Similarity	NPD7124	Phase 2
0.6795	Remote Similarity	NPD2120	Phase 2
0.679	Remote Similarity	NPD5563	Clinical (unspecified phase)
0.6781	Remote Similarity	NPD7018	Phase 2
0.6776	Remote Similarity	NPD2164	Clinical (unspecified phase)
0.6757	Remote Similarity	NPD5746	Approved
0.6753	Remote Similarity	NPD1044	Clinical (unspecified phase)
0.6748	Remote Similarity	NPD5353	Approved
0.6736	Remote Similarity	NPD2230	Approved
0.6736	Remote Similarity	NPD2233	Approved
0.6736	Remote Similarity	NPD2232	Approved
0.6731	Remote Similarity	NPD5307	Clinical (unspecified phase)
0.673	Remote Similarity	NPD5976	Discontinued
0.673	Remote Similarity	NPD6980	Clinical (unspecified phase)
0.6728	Remote Similarity	NPD7248	Discontinued
0.6726	Remote Similarity	NPD2898	Approved
0.6714	Remote Similarity	NPD3596	Phase 2
0.6711	Remote Similarity	NPD3374	Clinical (unspecified phase)
0.671	Remote Similarity	NPD5177	Phase 3
0.6709	Remote Similarity	NPD1424	Approved
0.669	Remote Similarity	NPD6382	Discontinued
0.669	Remote Similarity	NPD2595	Approved
0.669	Remote Similarity	NPD2594	Approved
0.6689	Remote Similarity	NPD4207	Discontinued
0.6687	Remote Similarity	NPD3687	Approved
0.6687	Remote Similarity	NPD5773	Approved
0.6687	Remote Similarity	NPD5772	Approved
0.6687	Remote Similarity	NPD3686	Approved
0.6687	Remote Similarity	NPD4585	Approved
0.6667	Remote Similarity	NPD7090	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD3647	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD7905	Discontinued
0.6667	Remote Similarity	NPD3530	Approved
0.6667	Remote Similarity	NPD3531	Approved
0.6667	Remote Similarity	NPD5745	Approved
0.6667	Remote Similarity	NPD6618	Phase 2
0.6667	Remote Similarity	NPD1975	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD776	Approved
0.6667	Remote Similarity	NPD5754	Discontinued
0.6667	Remote Similarity	NPD3532	Approved
0.6649	Remote Similarity	NPD7607	Clinical (unspecified phase)
0.6648	Remote Similarity	NPD6493	Phase 3
0.6646	Remote Similarity	NPD7261	Clinical (unspecified phase)
0.6646	Remote Similarity	NPD2560	Approved
0.6646	Remote Similarity	NPD2563	Approved
0.6646	Remote Similarity	NPD4017	Approved
0.6645	Remote Similarity	NPD7037	Approved
0.6645	Remote Similarity	NPD7153	Discontinued
0.6644	Remote Similarity	NPD7258	Clinical (unspecified phase)
0.6644	Remote Similarity	NPD5163	Phase 2
0.663	Remote Similarity	NPD4420	Approved
0.6629	Remote Similarity	NPD7296	Approved
0.6628	Remote Similarity	NPD6297	Approved
0.6627	Remote Similarity	NPD6365	Clinical (unspecified phase)
0.6625	Remote Similarity	NPD2122	Discontinued
0.6625	Remote Similarity	NPD6031	Approved
0.6625	Remote Similarity	NPD6030	Approved
0.6623	Remote Similarity	NPD1725	Approved
0.6622	Remote Similarity	NPD9494	Approved
0.6608	Remote Similarity	NPD5313	Approved
0.6608	Remote Similarity	NPD5312	Approved
0.6606	Remote Similarity	NPD5019	Clinical (unspecified phase)
0.6605	Remote Similarity	NPD7028	Phase 2
0.6604	Remote Similarity	NPD4123	Phase 3
0.6604	Remote Similarity	NPD2335	Discontinued
0.6603	Remote Similarity	NPD2654	Approved
0.6601	Remote Similarity	NPD7119	Phase 2
0.6597	Remote Similarity	NPD3447	Discontinued
0.6587	Remote Similarity	NPD2041	Clinical (unspecified phase)
0.6587	Remote Similarity	NPD5677	Discontinued
0.6587	Remote Similarity	NPD2042	Clinical (unspecified phase)
0.6584	Remote Similarity	NPD4124	Clinical (unspecified phase)
0.6582	Remote Similarity	NPD3281	Clinical (unspecified phase)
0.6582	Remote Similarity	NPD5295	Discontinued
0.6575	Remote Similarity	NPD5564	Approved
0.6573	Remote Similarity	NPD5691	Approved
0.6568	Remote Similarity	NPD5242	Approved
0.6564	Remote Similarity	NPD5090	Approved
0.6564	Remote Similarity	NPD5089	Approved
0.6562	Remote Similarity	NPD7314	Clinical (unspecified phase)
0.6561	Remote Similarity	NPD6331	Phase 2
0.6558	Remote Similarity	NPD4108	Discontinued
0.6556	Remote Similarity	NPD1726	Clinical (unspecified phase)
0.6554	Remote Similarity	NPD7291	Discontinued
0.6554	Remote Similarity	NPD7243	Clinical (unspecified phase)
0.6554	Remote Similarity	NPD6584	Phase 3
0.655	Remote Similarity	NPD2822	Clinical (unspecified phase)
0.6529	Remote Similarity	NPD4481	Phase 3
0.6528	Remote Similarity	NPD4626	Approved
0.6524	Remote Similarity	NPD3382	Approved
0.6524	Remote Similarity	NPD3383	Approved
0.6524	Remote Similarity	NPD3384	Approved
0.6522	Remote Similarity	NPD4727	Phase 1
0.6517	Remote Similarity	NPD6377	Clinical (unspecified phase)
0.6517	Remote Similarity	NPD7235	Clinical (unspecified phase)
0.6516	Remote Similarity	NPD6032	Approved
0.6513	Remote Similarity	NPD3109	Approved
0.6513	Remote Similarity	NPD3110	Approved
0.651	Remote Similarity	NPD2237	Approved
0.6507	Remote Similarity	NPD2981	Phase 2
0.6503	Remote Similarity	NPD6581	Approved
0.6503	Remote Similarity	NPD6580	Approved
0.6503	Remote Similarity	NPD2486	Discontinued
0.65	Remote Similarity	NPD1771	Clinical (unspecified phase)
0.6497	Remote Similarity	NPD4084	Clinical (unspecified phase)
0.6491	Remote Similarity	NPD5966	Clinical (unspecified phase)
0.649	Remote Similarity	NPD6812	Clinical (unspecified phase)
0.649	Remote Similarity	NPD5111	Phase 2
0.649	Remote Similarity	NPD5109	Approved
0.649	Remote Similarity	NPD5110	Phase 2
0.649	Remote Similarity	NPD1336	Approved
0.649	Remote Similarity	NPD1039	Discontinued
0.6489	Remote Similarity	NPD4859	Phase 1
0.6486	Remote Similarity	NPD5006	Approved
0.6486	Remote Similarity	NPD1820	Approved
0.6486	Remote Similarity	NPD1817	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