NPASS Compound

Structure

CID169398 OpenBabel06191715542D 37 39 0 0 1 0 0 0 0 0999 V2000 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 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 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 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 2 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 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 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 2 33 1 0 0 0 0 3 15 2 0 0 0 0 4 6 1 0 0 0 0 4 13 2 0 0 0 0 5 7 2 0 0 0 0 5 13 1 0 0 0 0 6 14 2 0 0 0 0 7 14 1 0 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 34 1 0 0 0 0 10 19 1 0 0 0 0 11 26 1 0 0 0 0 12 17 2 0 0 0 0 12 35 1 0 0 0 0 14 27 1 0 0 0 0 15 16 1 0 0 0 0 15 24 1 0 0 0 0 16 10 1 1 0 0 0 16 17 1 0 0 0 0 17 23 1 0 0 0 0 18 11 1 6 0 0 0 18 20 1 0 0 0 0 18 36 1 0 0 0 0 19 28 2 0 0 0 0 19 34 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 1 0 0 0 21 22 1 0 0 0 0 21 30 1 6 0 0 0 22 25 1 0 0 0 0 22 31 1 1 0 0 0 23 32 2 0 0 0 0 23 33 1 0 0 0 0 24 35 1 0 0 0 0 24 37 1 6 0 0 0 25 36 1 0 0 0 0 25 37 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	524.19
Volume:	502.314
LogP:	0.837
LogD:	0.868
LogS:	-1.642
# Rotatable Bonds:	11
TPSA:	181.44
# H-Bond Aceptor:	12
# H-Bond Donor:	5
# Rings:	3
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.21
Synthetic Accessibility Score:	4.574
Fsp3:	0.52
Lipinski Rule-of-5:	Rejected
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:	-5.577
MDCK Permeability:	9.27318396861665e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.977
Human Intestinal Absorption (HIA):	0.886
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.271
Plasma Protein Binding (PPB):	61.497955322265625%
Volume Distribution (VD):	0.338
Pgp-substrate:	22.286766052246094%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.091
CYP2C19-inhibitor:	0.077
CYP2C19-substrate:	0.101
CYP2C9-inhibitor:	0.077
CYP2C9-substrate:	0.071
CYP2D6-inhibitor:	0.062
CYP2D6-substrate:	0.094
CYP3A4-inhibitor:	0.096
CYP3A4-substrate:	0.2

ADMET: Excretion

Clearance (CL):	2.91
Half-life (T1/2):	0.89

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.254
Drug-inuced Liver Injury (DILI):	0.938
AMES Toxicity:	0.824
Rat Oral Acute Toxicity:	0.406
Maximum Recommended Daily Dose:	0.935
Skin Sensitization:	0.247
Carcinogencity:	0.914
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.905

Download Data

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

Natural Product: NPC169398

Natural Product ID:	NPC169398
*Common Name:**	Ligstroside
IUPAC Name:	methyl (4S,5E,6S)-5-ethylidene-4-[2-[2-(4-hydroxyphenyl)ethoxy]-2-oxoethyl]-6-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4H-pyran-3-carboxylate
Synonyms:	Ligstroside
Standard InCHIKey:	GMQXOLRKJQWPNB-MVVLSVRYSA-N
Standard InCHI:	InChI=1S/C25H32O12/c1-3-15-16(10-19(28)34-9-8-13-4-6-14(27)7-5-13)17(23(32)33-2)12-35-24(15)37-25-22(31)21(30)20(29)18(11-26)36-25/h3-7,12,16,18,20-22,24-27,29-31H,8-11H2,1-2H3/b15-3+/t16-,18+,20+,21-,22+,24-,25-/m0/s1
SMILES:	C/C=C/1[C@H](CC(=O)OCCc2ccc(cc2)O)C(=CO[C@H]1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1086877
PubChem CID:	14136859
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides

*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
NPO18340	Ligustrum lucidum	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[11411539]
NPO19884	Fraxinus excelsior	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20000781]
NPO16259	Syringa reticulata	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21955940]
NPO19935	Evodia rutaecarpa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7463094]
NPO19935	Evodia rutaecarpa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8201313]
NPO19935	Evodia rutaecarpa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8699182]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18340	Ligustrum lucidum	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9661	Fraxinus szaboana	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3564	Fraxinus stylosa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18105	Fructus ligustri lucidi	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9661	Fraxinus szaboana	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15212.1	Fraxinus chinensis subsp. rhynchophylla	Subspecies	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18340	Ligustrum lucidum	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3564	Fraxinus stylosa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19935	Evodia rutaecarpa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9661	Fraxinus szaboana	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18340	Ligustrum lucidum	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3564	Fraxinus stylosa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16845	Euodia bodinieri	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19935	Evodia rutaecarpa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15212.1	Fraxinus chinensis subsp. rhynchophylla	Subspecies	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3564	Fraxinus stylosa	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18340	Ligustrum lucidum	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9661	Fraxinus szaboana	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4877	Euodia officinalis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8314	Euodia ruticarpa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18340	Ligustrum lucidum	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13914	Fraxinus ornus	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15212.1	Fraxinus chinensis subsp. rhynchophylla	Subspecies	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19935	Evodia rutaecarpa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19884	Fraxinus excelsior	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16259	Syringa reticulata	Species	Oleaceae	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	1
Others	3

Activity Type	# Activity
Cell Line	4
NON-MOLECULAR	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT520	Cell Line	3T3-L1	Mus musculus	Inhibition	=	-9.3	%	PMID[570538]
NPT520	Cell Line	3T3-L1	Mus musculus	Inhibition	=	-76.4	%	PMID[570538]
NPT520	Cell Line	3T3-L1	Mus musculus	Inhibition	=	-9.8	%	PMID[570538]
NPT134	Cell Line	SK-BR-3	Homo sapiens	IC50	>	20000.0	nM	PMID[570540]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	EC50	>	100000.0	nM	PMID[570539]
NPT1	Others	Radical scavenging activity		EC50	>	100000.0	nM	PMID[570539]

☑ 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 NPC169398 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	264
0.1-0.2	1024
0.2-0.3	2670
0.3-0.4	6327
0.4-0.5	10593
0.5-0.6	7311
0.6-0.7	11427
0.7-0.8	2764
0.8-0.85	216
0.85-0.9	83
0.9-0.95	13
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
0.9769	High Similarity	NPC101686
0.9769	High Similarity	NPC469364
0.9769	High Similarity	NPC65262
0.9478	High Similarity	NPC296643
0.9203	High Similarity	NPC212808
0.9197	High Similarity	NPC202391
0.9197	High Similarity	NPC296659
0.9154	High Similarity	NPC469549
0.9124	High Similarity	NPC469367
0.9111	High Similarity	NPC220936
0.9111	High Similarity	NPC31745
0.9104	High Similarity	NPC472132
0.9071	High Similarity	NPC23677
0.9015	High Similarity	NPC235294
0.9015	High Similarity	NPC46137
0.9	High Similarity	NPC288416
0.9	High Similarity	NPC106677
0.8986	High Similarity	NPC293154
0.8929	High Similarity	NPC475539
0.8929	High Similarity	NPC119773
0.8929	High Similarity	NPC474268
0.8929	High Similarity	NPC143246
0.8923	High Similarity	NPC471157
0.8921	High Similarity	NPC251062
0.8921	High Similarity	NPC63304
0.8921	High Similarity	NPC184464
0.8906	High Similarity	NPC52097
0.8873	High Similarity	NPC96599
0.8872	High Similarity	NPC225384
0.8872	High Similarity	NPC281798
0.8872	High Similarity	NPC138777
0.8872	High Similarity	NPC254819
0.8872	High Similarity	NPC246869
0.8872	High Similarity	NPC478255
0.8864	High Similarity	NPC253595
0.8857	High Similarity	NPC475528
0.8855	High Similarity	NPC173150
0.8855	High Similarity	NPC471881
0.8855	High Similarity	NPC471882
0.8855	High Similarity	NPC156692
0.8855	High Similarity	NPC45224
0.8855	High Similarity	NPC35288
0.8849	High Similarity	NPC475213
0.8849	High Similarity	NPC152796
0.8849	High Similarity	NPC186296
0.8846	High Similarity	NPC126991
0.8846	High Similarity	NPC83218
0.8828	High Similarity	NPC11724
0.8824	High Similarity	NPC471345
0.8811	High Similarity	NPC240592
0.8811	High Similarity	NPC117346
0.8788	High Similarity	NPC225307
0.8786	High Similarity	NPC77922
0.8786	High Similarity	NPC473281
0.8779	High Similarity	NPC252114
0.8779	High Similarity	NPC61181
0.875	High Similarity	NPC476872
0.875	High Similarity	NPC263829
0.8741	High Similarity	NPC114116
0.8714	High Similarity	NPC478250
0.8712	High Similarity	NPC103533
0.8705	High Similarity	NPC154262
0.8705	High Similarity	NPC7518
0.8705	High Similarity	NPC137501
0.8705	High Similarity	NPC159387
0.8696	High Similarity	NPC49597
0.8676	High Similarity	NPC471029
0.8662	High Similarity	NPC473147
0.8621	High Similarity	NPC474620
0.8621	High Similarity	NPC289021
0.8621	High Similarity	NPC158546
0.8611	High Similarity	NPC478234
0.8601	High Similarity	NPC473149
0.8582	High Similarity	NPC295970
0.8561	High Similarity	NPC81515
0.8561	High Similarity	NPC89105
0.8561	High Similarity	NPC64141
0.8561	High Similarity	NPC476383
0.8561	High Similarity	NPC123704
0.8561	High Similarity	NPC68092
0.8561	High Similarity	NPC197316
0.8561	High Similarity	NPC472350
0.8552	High Similarity	NPC69367
0.854	High Similarity	NPC287597
0.854	High Similarity	NPC34293
0.854	High Similarity	NPC886
0.8538	High Similarity	NPC55608
0.8538	High Similarity	NPC469686
0.8531	High Similarity	NPC291153
0.8529	High Similarity	NPC473285
0.8527	High Similarity	NPC282409
0.8527	High Similarity	NPC469702
0.8521	High Similarity	NPC194938
0.8519	High Similarity	NPC469705
0.8519	High Similarity	NPC470122
0.8519	High Similarity	NPC17968
0.8514	High Similarity	NPC475484
0.8504	High Similarity	NPC148055
0.8493	Intermediate Similarity	NPC475379
0.8489	Intermediate Similarity	NPC260425
0.8489	Intermediate Similarity	NPC476376
0.8483	Intermediate Similarity	NPC478236
0.8483	Intermediate Similarity	NPC478242
0.8478	Intermediate Similarity	NPC476870
0.8467	Intermediate Similarity	NPC28637
0.8462	Intermediate Similarity	NPC469704
0.8462	Intermediate Similarity	NPC469548
0.8462	Intermediate Similarity	NPC160854
0.8462	Intermediate Similarity	NPC469703
0.8462	Intermediate Similarity	NPC476448
0.8462	Intermediate Similarity	NPC201402
0.8462	Intermediate Similarity	NPC476445
0.8451	Intermediate Similarity	NPC116104
0.8451	Intermediate Similarity	NPC88754
0.8451	Intermediate Similarity	NPC237872
0.8451	Intermediate Similarity	NPC263397
0.8451	Intermediate Similarity	NPC204644
0.8451	Intermediate Similarity	NPC302286
0.8444	Intermediate Similarity	NPC477293
0.8444	Intermediate Similarity	NPC477294
0.8444	Intermediate Similarity	NPC229784
0.844	Intermediate Similarity	NPC134405
0.844	Intermediate Similarity	NPC476377
0.844	Intermediate Similarity	NPC47471
0.844	Intermediate Similarity	NPC476385
0.844	Intermediate Similarity	NPC80098
0.844	Intermediate Similarity	NPC46644
0.8435	Intermediate Similarity	NPC203664
0.8429	Intermediate Similarity	NPC328273
0.8429	Intermediate Similarity	NPC321184
0.8429	Intermediate Similarity	NPC321638
0.8429	Intermediate Similarity	NPC205195
0.8429	Intermediate Similarity	NPC171134
0.8429	Intermediate Similarity	NPC220942
0.8425	Intermediate Similarity	NPC182350
0.8425	Intermediate Similarity	NPC35097
0.8417	Intermediate Similarity	NPC166180
0.8414	Intermediate Similarity	NPC120728
0.8406	Intermediate Similarity	NPC471883
0.8406	Intermediate Similarity	NPC34456
0.8403	Intermediate Similarity	NPC320734
0.8394	Intermediate Similarity	NPC471066
0.8394	Intermediate Similarity	NPC471095
0.8392	Intermediate Similarity	NPC471028
0.838	Intermediate Similarity	NPC148080
0.838	Intermediate Similarity	NPC469623
0.838	Intermediate Similarity	NPC140502
0.838	Intermediate Similarity	NPC222433
0.838	Intermediate Similarity	NPC265648
0.8378	Intermediate Similarity	NPC246893
0.837	Intermediate Similarity	NPC232880
0.837	Intermediate Similarity	NPC158673
0.8369	Intermediate Similarity	NPC475530
0.8369	Intermediate Similarity	NPC473799
0.8359	Intermediate Similarity	NPC175771
0.8357	Intermediate Similarity	NPC78363
0.8357	Intermediate Similarity	NPC310252
0.8357	Intermediate Similarity	NPC84789
0.8357	Intermediate Similarity	NPC302583
0.8357	Intermediate Similarity	NPC100558
0.8346	Intermediate Similarity	NPC157338
0.8346	Intermediate Similarity	NPC313193
0.8345	Intermediate Similarity	NPC97240
0.8345	Intermediate Similarity	NPC123988
0.8344	Intermediate Similarity	NPC179914
0.8344	Intermediate Similarity	NPC469384
0.8333	Intermediate Similarity	NPC210330
0.8333	Intermediate Similarity	NPC100998
0.8333	Intermediate Similarity	NPC34927
0.8333	Intermediate Similarity	NPC471067
0.8333	Intermediate Similarity	NPC252292
0.8333	Intermediate Similarity	NPC164172
0.8333	Intermediate Similarity	NPC476142
0.8333	Intermediate Similarity	NPC34587
0.8333	Intermediate Similarity	NPC476382
0.8333	Intermediate Similarity	NPC254398
0.8333	Intermediate Similarity	NPC475378
0.8322	Intermediate Similarity	NPC476381
0.8322	Intermediate Similarity	NPC269141
0.8322	Intermediate Similarity	NPC96795
0.8322	Intermediate Similarity	NPC476384
0.8322	Intermediate Similarity	NPC298257
0.8322	Intermediate Similarity	NPC119537
0.8322	Intermediate Similarity	NPC247032
0.8322	Intermediate Similarity	NPC476397
0.8322	Intermediate Similarity	NPC476375
0.8322	Intermediate Similarity	NPC476380
0.8322	Intermediate Similarity	NPC264632
0.8322	Intermediate Similarity	NPC476378
0.8322	Intermediate Similarity	NPC175214
0.8322	Intermediate Similarity	NPC76406
0.8322	Intermediate Similarity	NPC205864
0.8322	Intermediate Similarity	NPC112
0.8321	Intermediate Similarity	NPC219677
0.8311	Intermediate Similarity	NPC194705
0.831	Intermediate Similarity	NPC79908
0.8299	Intermediate Similarity	NPC12006
0.8298	Intermediate Similarity	NPC62800
0.8298	Intermediate Similarity	NPC324262
0.8296	Intermediate Similarity	NPC476873

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 NPC169398 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	224
0.1-0.2	699
0.2-0.3	1559
0.3-0.4	2715
0.4-0.5	2123
0.5-0.6	1281
0.6-0.7	508
0.7-0.8	40
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8561	High Similarity	NPD7266	Discontinued
0.7806	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.7748	Intermediate Similarity	NPD1653	Approved
0.7721	Intermediate Similarity	NPD1091	Approved
0.7703	Intermediate Similarity	NPD6190	Approved
0.7669	Intermediate Similarity	NPD7685	Pre-registration
0.7613	Intermediate Similarity	NPD8455	Phase 2
0.7586	Intermediate Similarity	NPD7097	Phase 1
0.7586	Intermediate Similarity	NPD4978	Clinical (unspecified phase)
0.7556	Intermediate Similarity	NPD9545	Approved
0.7517	Intermediate Similarity	NPD4628	Phase 3
0.7485	Intermediate Similarity	NPD7054	Approved
0.7485	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.7439	Intermediate Similarity	NPD7472	Approved
0.7431	Intermediate Similarity	NPD6233	Phase 2
0.7423	Intermediate Similarity	NPD7228	Approved
0.7419	Intermediate Similarity	NPD4380	Phase 2
0.7379	Intermediate Similarity	NPD7966	Clinical (unspecified phase)
0.7368	Intermediate Similarity	NPD6143	Clinical (unspecified phase)
0.7361	Intermediate Similarity	NPD6859	Clinical (unspecified phase)
0.7358	Intermediate Similarity	NPD7075	Discontinued
0.7349	Intermediate Similarity	NPD7251	Discontinued
0.7333	Intermediate Similarity	NPD7074	Phase 3
0.7333	Intermediate Similarity	NPD1652	Phase 2
0.7325	Intermediate Similarity	NPD37	Approved
0.7317	Intermediate Similarity	NPD3818	Discontinued
0.7312	Intermediate Similarity	NPD6234	Discontinued
0.7305	Intermediate Similarity	NPD7808	Phase 3
0.7305	Intermediate Similarity	NPD4338	Clinical (unspecified phase)
0.7297	Intermediate Similarity	NPD7033	Discontinued
0.7296	Intermediate Similarity	NPD4967	Phase 2
0.7296	Intermediate Similarity	NPD4966	Approved
0.7296	Intermediate Similarity	NPD4965	Approved
0.7289	Intermediate Similarity	NPD6797	Phase 2
0.7279	Intermediate Similarity	NPD6653	Approved
0.7246	Intermediate Similarity	NPD6559	Discontinued
0.7241	Intermediate Similarity	NPD6798	Discontinued
0.7219	Intermediate Similarity	NPD7421	Clinical (unspecified phase)
0.7215	Intermediate Similarity	NPD6801	Discontinued
0.7211	Intermediate Similarity	NPD6355	Discontinued
0.7211	Intermediate Similarity	NPD5124	Phase 1
0.7211	Intermediate Similarity	NPD5123	Clinical (unspecified phase)
0.7211	Intermediate Similarity	NPD230	Phase 1
0.7208	Intermediate Similarity	NPD8389	Clinical (unspecified phase)
0.7188	Intermediate Similarity	NPD4868	Clinical (unspecified phase)
0.7183	Intermediate Similarity	NPD3225	Approved
0.7176	Intermediate Similarity	NPD8055	Clinical (unspecified phase)
0.7171	Intermediate Similarity	NPD1878	Clinical (unspecified phase)
0.717	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.716	Intermediate Similarity	NPD8312	Approved
0.716	Intermediate Similarity	NPD8313	Approved
0.7134	Intermediate Similarity	NPD7458	Discontinued
0.7123	Intermediate Similarity	NPD3268	Approved
0.7121	Intermediate Similarity	NPD1358	Approved
0.7117	Intermediate Similarity	NPD7199	Phase 2
0.7115	Intermediate Similarity	NPD5403	Approved
0.7111	Intermediate Similarity	NPD7843	Approved
0.7095	Intermediate Similarity	NPD4340	Discontinued
0.7092	Intermediate Similarity	NPD422	Phase 1
0.7075	Intermediate Similarity	NPD4062	Phase 3
0.7069	Intermediate Similarity	NPD7879	Clinical (unspecified phase)
0.7059	Intermediate Similarity	NPD8166	Discontinued
0.7055	Intermediate Similarity	NPD3027	Phase 3
0.7045	Intermediate Similarity	NPD3134	Approved
0.7044	Intermediate Similarity	NPD7411	Suspended
0.7041	Intermediate Similarity	NPD7240	Approved
0.7037	Intermediate Similarity	NPD969	Suspended
0.7034	Intermediate Similarity	NPD5736	Approved
0.7032	Intermediate Similarity	NPD6799	Approved
0.7014	Intermediate Similarity	NPD2797	Approved
0.7014	Intermediate Similarity	NPD6362	Approved
0.7007	Intermediate Similarity	NPD3764	Approved
0.7006	Intermediate Similarity	NPD6980	Clinical (unspecified phase)
0.6993	Remote Similarity	NPD6674	Discontinued
0.6987	Remote Similarity	NPD5401	Approved
0.6968	Remote Similarity	NPD5058	Phase 3
0.6966	Remote Similarity	NPD5647	Approved
0.6957	Remote Similarity	NPD7157	Approved
0.695	Remote Similarity	NPD5125	Phase 3
0.695	Remote Similarity	NPD5126	Approved
0.6948	Remote Similarity	NPD6398	Clinical (unspecified phase)
0.694	Remote Similarity	NPD2684	Approved
0.6939	Remote Similarity	NPD7095	Approved
0.6937	Remote Similarity	NPD7615	Clinical (unspecified phase)
0.6928	Remote Similarity	NPD970	Clinical (unspecified phase)
0.6928	Remote Similarity	NPD7184	Clinical (unspecified phase)
0.6928	Remote Similarity	NPD1549	Phase 2
0.6914	Remote Similarity	NPD8443	Clinical (unspecified phase)
0.6914	Remote Similarity	NPD5402	Approved
0.6914	Remote Similarity	NPD3817	Phase 2
0.6913	Remote Similarity	NPD1613	Approved
0.6913	Remote Similarity	NPD1612	Clinical (unspecified phase)
0.6913	Remote Similarity	NPD4060	Phase 1
0.6901	Remote Similarity	NPD3847	Discontinued
0.6894	Remote Similarity	NPD1934	Approved
0.6879	Remote Similarity	NPD7004	Clinical (unspecified phase)
0.6875	Remote Similarity	NPD4379	Clinical (unspecified phase)
0.6871	Remote Similarity	NPD4908	Phase 1
0.6866	Remote Similarity	NPD9265	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD6004	Phase 3
0.6863	Remote Similarity	NPD6003	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD6005	Phase 3
0.6863	Remote Similarity	NPD6006	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD6002	Phase 3
0.6863	Remote Similarity	NPD1552	Clinical (unspecified phase)
0.6863	Remote Similarity	NPD1550	Clinical (unspecified phase)
0.6853	Remote Similarity	NPD3705	Approved
0.6853	Remote Similarity	NPD1535	Discovery
0.6852	Remote Similarity	NPD2393	Clinical (unspecified phase)
0.6852	Remote Similarity	NPD7819	Suspended
0.6849	Remote Similarity	NPD6007	Clinical (unspecified phase)
0.6846	Remote Similarity	NPD6663	Approved
0.6842	Remote Similarity	NPD1510	Phase 2
0.6839	Remote Similarity	NPD3750	Approved
0.6831	Remote Similarity	NPD1778	Approved
0.6818	Remote Similarity	NPD6647	Phase 2
0.6818	Remote Similarity	NPD2424	Discontinued
0.6809	Remote Similarity	NPD1548	Phase 1
0.6809	Remote Similarity	NPD1894	Discontinued
0.6807	Remote Similarity	NPD8127	Discontinued
0.6806	Remote Similarity	NPD1481	Phase 2
0.6806	Remote Similarity	NPD1608	Approved
0.6803	Remote Similarity	NPD2861	Phase 2
0.6797	Remote Similarity	NPD2935	Discontinued
0.6786	Remote Similarity	NPD6166	Phase 2
0.6786	Remote Similarity	NPD9493	Approved
0.6786	Remote Similarity	NPD6167	Clinical (unspecified phase)
0.6786	Remote Similarity	NPD6168	Clinical (unspecified phase)
0.6784	Remote Similarity	NPD7993	Clinical (unspecified phase)
0.6781	Remote Similarity	NPD3266	Approved
0.6781	Remote Similarity	NPD3267	Approved
0.6779	Remote Similarity	NPD4907	Clinical (unspecified phase)
0.6776	Remote Similarity	NPD4537	Clinical (unspecified phase)
0.6776	Remote Similarity	NPD4538	Approved
0.6776	Remote Similarity	NPD4536	Approved
0.6772	Remote Similarity	NPD4378	Clinical (unspecified phase)
0.677	Remote Similarity	NPD6599	Discontinued
0.6765	Remote Similarity	NPD5844	Phase 1
0.6763	Remote Similarity	NPD2629	Approved
0.6761	Remote Similarity	NPD8397	Clinical (unspecified phase)
0.6761	Remote Similarity	NPD1357	Approved
0.6757	Remote Similarity	NPD6832	Phase 2
0.6755	Remote Similarity	NPD1933	Approved
0.6753	Remote Similarity	NPD5763	Approved
0.6753	Remote Similarity	NPD5762	Approved
0.6752	Remote Similarity	NPD6652	Clinical (unspecified phase)
0.6748	Remote Similarity	NPD2801	Approved
0.6741	Remote Similarity	NPD290	Approved
0.6739	Remote Similarity	NPD5535	Approved
0.6736	Remote Similarity	NPD1610	Phase 2
0.672	Remote Similarity	NPD7585	Approved
0.6716	Remote Similarity	NPD5048	Discontinued
0.6712	Remote Similarity	NPD8651	Approved
0.6706	Remote Similarity	NPD3751	Discontinued
0.6691	Remote Similarity	NPD1241	Discontinued
0.6689	Remote Similarity	NPD1240	Approved
0.6688	Remote Similarity	NPD2796	Approved
0.6688	Remote Similarity	NPD2239	Approved
0.6688	Remote Similarity	NPD2438	Suspended
0.6688	Remote Similarity	NPD2240	Approved
0.6686	Remote Similarity	NPD7852	Clinical (unspecified phase)
0.6685	Remote Similarity	NPD7435	Discontinued
0.6667	Remote Similarity	NPD7583	Approved
0.6667	Remote Similarity	NPD694	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD3496	Discontinued
0.6667	Remote Similarity	NPD3787	Discontinued
0.6667	Remote Similarity	NPD2933	Approved
0.6667	Remote Similarity	NPD3094	Phase 2
0.6667	Remote Similarity	NPD7768	Phase 2
0.6667	Remote Similarity	NPD2934	Approved
0.6667	Remote Similarity	NPD7410	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD3536	Discontinued
0.6649	Remote Similarity	NPD8320	Phase 1
0.6649	Remote Similarity	NPD8319	Approved
0.6648	Remote Similarity	NPD8150	Discontinued
0.6648	Remote Similarity	NPD7237	Clinical (unspecified phase)
0.6648	Remote Similarity	NPD8434	Phase 2
0.6647	Remote Similarity	NPD7473	Discontinued
0.6646	Remote Similarity	NPD7440	Discontinued
0.6644	Remote Similarity	NPD1529	Clinical (unspecified phase)
0.6644	Remote Similarity	NPD3685	Discontinued
0.6643	Remote Similarity	NPD5585	Approved
0.6642	Remote Similarity	NPD5909	Discontinued
0.6642	Remote Similarity	NPD2067	Discontinued
0.6625	Remote Similarity	NPD7314	Clinical (unspecified phase)
0.6624	Remote Similarity	NPD4110	Phase 3
0.6624	Remote Similarity	NPD4109	Clinical (unspecified phase)
0.6623	Remote Similarity	NPD5960	Phase 3
0.6623	Remote Similarity	NPD5588	Approved
0.6622	Remote Similarity	NPD2798	Approved
0.6615	Remote Similarity	NPD2859	Approved
0.6615	Remote Similarity	NPD2860	Approved
0.6606	Remote Similarity	NPD5353	Approved
0.6605	Remote Similarity	NPD3455	Phase 2
0.6604	Remote Similarity	NPD1511	Approved
0.6603	Remote Similarity	NPD5958	Discontinued
0.6603	Remote Similarity	NPD4534	Discontinued
0.6601	Remote Similarity	NPD1607	Approved
0.66	Remote Similarity	NPD3136	Phase 2
0.66	Remote Similarity	NPD5952	Clinical (unspecified phase)

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