NPASS Compound

Structure

CID40488 OpenBabel06191715372D 30 34 0 0 1 0 0 0 0 0999 V2000 -8.6334 -1.5848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3797 1.0125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9669 0.9709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8761 0.5061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8443 -1.4638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0004 -1.9513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2248 -1.4628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3803 -1.9506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8450 1.4627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 0.9753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9535 -1.7618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6893 -0.0004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6902 0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6402 -0.2184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7424 -1.1884 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3799 0.0007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0691 0.0010 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8445 -0.4879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6895 0.9749 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2246 -0.4869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5351 -1.4631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8454 -1.4634 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5349 -0.4872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8452 -0.4875 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0624 -1.3654 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9602 -0.3954 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.7491 0.1780 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5758 1.4862 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2735 -1.9388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 16 1 0 0 0 0 5 6 1 0 0 0 0 5 18 2 0 0 0 0 7 8 2 0 0 0 0 7 20 1 0 0 0 0 8 21 1 0 0 0 0 9 10 1 0 0 0 0 9 19 1 0 0 0 0 10 27 1 0 0 0 0 11 15 1 0 0 0 0 11 25 1 0 0 0 0 12 18 1 0 0 0 0 12 19 1 0 0 0 0 13 23 1 0 0 0 0 13 24 1 0 0 0 0 14 15 1 0 0 0 0 14 28 1 0 0 0 0 15 1 1 6 0 0 0 16 20 2 0 0 0 0 16 23 1 0 0 0 0 17 3 1 1 0 0 0 17 20 1 0 0 0 0 18 27 1 0 0 0 0 19 29 1 6 0 0 0 21 22 1 0 0 0 0 21 23 2 0 0 0 0 22 6 1 1 0 0 0 22 24 1 0 0 0 0 24 27 1 6 0 0 0 25 26 1 0 0 0 0 25 30 1 6 0 0 0 26 17 1 1 0 0 0 26 28 1 0 0 0 0 27 4 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	409.3
Volume:	450.797
LogP:	5.111
LogD:	3.828
LogS:	-5.064
# Rotatable Bonds:	2
TPSA:	52.49
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.626
Synthetic Accessibility Score:	4.86
Fsp3:	0.704
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.066
MDCK Permeability:	7.499188996007433e-06
Pgp-inhibitor:	0.967
Pgp-substrate:	0.992
Human Intestinal Absorption (HIA):	0.021
20% Bioavailability (F20%):	0.986
30% Bioavailability (F30%):	0.07

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.514
Plasma Protein Binding (PPB):	94.63874053955078%
Volume Distribution (VD):	1.96
Pgp-substrate:	5.199273109436035%

ADMET: Metabolism

CYP1A2-inhibitor:	0.088
CYP1A2-substrate:	0.688
CYP2C19-inhibitor:	0.249
CYP2C19-substrate:	0.941
CYP2C9-inhibitor:	0.102
CYP2C9-substrate:	0.187
CYP2D6-inhibitor:	0.277
CYP2D6-substrate:	0.889
CYP3A4-inhibitor:	0.678
CYP3A4-substrate:	0.406

ADMET: Excretion

Clearance (CL):	10.59
Half-life (T1/2):	0.074

ADMET: Toxicity

hERG Blockers:	0.866
Human Hepatotoxicity (H-HT):	0.318
Drug-inuced Liver Injury (DILI):	0.05
AMES Toxicity:	0.129
Rat Oral Acute Toxicity:	0.703
Maximum Recommended Daily Dose:	0.933
Skin Sensitization:	0.422
Carcinogencity:	0.577
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.957

Download Data

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

Natural Product: NPC40488

Natural Product ID:	NPC40488
*Common Name:**	Veratramine
IUPAC Name:	(2S,3R,5S)-2-[(1S)-1-[(3S,6aR,11aS,11bR)-3-hydroxy-10,11b-dimethyl-1,2,3,4,6,6a,11,11a-octahydrobenzo[a]fluoren-9-yl]ethyl]-5-methylpiperidin-3-ol
Synonyms:	Veratramine
Standard InCHIKey:	MALFODICFSIXPO-KFKQDBFTSA-N
Standard InCHI:	InChI=1S/C27H39NO2/c1-15-11-25(30)26(28-14-15)17(3)20-7-8-21-22-6-5-18-12-19(29)9-10-27(18,4)24(22)13-23(21)16(20)2/h5,7-8,15,17,19,22,24-26,28-30H,6,9-14H2,1-4H3/p+1/t15-,17-,19-,22-,24-,25+,26-,27-/m0/s1
SMILES:	C[C@H]1C[C@H]([C@H]([C@@H](C)c2ccc3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4Cc3c2C)O)[NH2+]C1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL464724
PubChem CID:	6070
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000020] Fluorenes

*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
NPO4347	Artemisia chinensis	Species	Asteraceae	Eukaryota	n.a.	leaf	n.a.	PMID[24689280]
NPO4347	Artemisia chinensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24689280]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	roots and rhizomes	n.a.	n.a.	PMID[25835537]
NPO11185	Hohenbuehelia grisea	Species	Pleurotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29356520]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27004	Veratrum viride	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4897	Veratrum grandiflorum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9049	Tanacetum parthenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4897	Veratrum grandiflorum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27004	Veratrum viride	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4347	Artemisia chinensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9049	Tanacetum parthenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27004	Veratrum viride	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29805	Veratrum grandiflo	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5651	Veratrum oxysepalum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4897	Veratrum grandiflorum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27004	Veratrum viride	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11185	Hohenbuehelia grisea	Species	Pleurotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5651	Veratrum oxysepalum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15380	Melicope ternata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9049	Tanacetum parthenium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4347	Artemisia chinensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2906	Leptactina senegambica	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4179	Uta tuberculata	Species	Iguanidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9996	Garcinia quaesita	Species	Clusiaceae	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
GI50	56
IC50	2
Others	2

Activity Type	# Activity
Cell Line	56
Individual Protein	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT367	Cell Line	MDA-N	Homo sapiens	GI50	n.a.	15703.63	nM	PMID[546035]
NPT368	Cell Line	SN12C	Homo sapiens	GI50	n.a.	20417.38	nM	PMID[546035]
NPT369	Cell Line	ACHN	Homo sapiens	GI50	n.a.	15031.42	nM	PMID[546035]
NPT370	Cell Line	NCI-H23	Homo sapiens	GI50	n.a.	11721.95	nM	PMID[546035]
NPT372	Cell Line	HOP-92	Homo sapiens	GI50	n.a.	2070.14	nM	PMID[546035]
NPT371	Cell Line	UO-31	Homo sapiens	GI50	n.a.	13995.87	nM	PMID[546035]
NPT90	Cell Line	DU-145	Homo sapiens	GI50	n.a.	27605.78	nM	PMID[546035]
NPT373	Cell Line	SK-MEL-5	Homo sapiens	GI50	n.a.	10814.34	nM	PMID[546035]
NPT375	Cell Line	Malme-3M	Homo sapiens	GI50	n.a.	16218.1	nM	PMID[546035]
NPT111	Cell Line	K562	Homo sapiens	GI50	n.a.	12078.14	nM	PMID[546035]
NPT376	Cell Line	A498	Homo sapiens	GI50	n.a.	15205.48	nM	PMID[546035]
NPT112	Cell Line	MOLT-4	Homo sapiens	GI50	n.a.	13122.0	nM	PMID[546035]
NPT377	Cell Line	OVCAR-3	Homo sapiens	GI50	n.a.	15631.48	nM	PMID[546035]
NPT378	Cell Line	NCI/ADR-RES	Homo sapiens	GI50	n.a.	23388.37	nM	PMID[546035]
NPT379	Cell Line	HOP-62	Homo sapiens	GI50	n.a.	23442.29	nM	PMID[546035]
NPT381	Cell Line	OVCAR-8	Homo sapiens	GI50	n.a.	21877.62	nM	PMID[546035]
NPT380	Cell Line	U-251	Homo sapiens	GI50	n.a.	14028.14	nM	PMID[546035]
NPT383	Cell Line	SNB-19	Homo sapiens	GI50	n.a.	27797.13	nM	PMID[546035]
NPT382	Cell Line	OVCAR-5	Homo sapiens	GI50	n.a.	17823.79	nM	PMID[546035]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	GI50	n.a.	16405.9	nM	PMID[546035]
NPT384	Cell Line	TK-10	Homo sapiens	GI50	n.a.	24378.11	nM	PMID[546035]
NPT323	Cell Line	SW-620	Homo sapiens	GI50	n.a.	28641.78	nM	PMID[546035]
NPT386	Cell Line	KM12	Homo sapiens	GI50	n.a.	14487.72	nM	PMID[546035]
NPT455	Cell Line	NCI-H522	Homo sapiens	GI50	n.a.	12971.79	nM	PMID[546035]
NPT387	Cell Line	M14	Homo sapiens	GI50	n.a.	15667.51	nM	PMID[546035]
NPT388	Cell Line	NCI-H322M	Homo sapiens	GI50	n.a.	11885.02	nM	PMID[546035]
NPT389	Cell Line	RPMI-8226	Homo sapiens	GI50	n.a.	3288.52	nM	PMID[546035]
NPT456	Cell Line	OVCAR-4	Homo sapiens	GI50	n.a.	12618.28	nM	PMID[546035]
NPT390	Cell Line	LOX IMVI	Homo sapiens	GI50	n.a.	11614.49	nM	PMID[546035]
NPT457	Cell Line	BT-549	Homo sapiens	GI50	n.a.	21134.89	nM	PMID[546035]
NPT391	Cell Line	HCC 2998	Homo sapiens	GI50	n.a.	13182.57	nM	PMID[546035]
NPT81	Cell Line	A549	Homo sapiens	GI50	n.a.	16672.47	nM	PMID[546035]
NPT392	Cell Line	SNB-75	Homo sapiens	GI50	n.a.	17458.22	nM	PMID[546035]
NPT393	Cell Line	HCT-116	Homo sapiens	GI50	n.a.	14321.88	nM	PMID[546035]
NPT148	Cell Line	HCT-15	Homo sapiens	GI50	n.a.	20183.66	nM	PMID[546035]
NPT394	Cell Line	EKVX	Homo sapiens	GI50	n.a.	2338.84	nM	PMID[546035]
NPT395	Cell Line	SF-268	Homo sapiens	GI50	n.a.	27733.2	nM	PMID[546035]
NPT306	Cell Line	PC-3	Homo sapiens	GI50	n.a.	11534.53	nM	PMID[546035]
NPT83	Cell Line	MCF7	Homo sapiens	GI50	n.a.	15417.0	nM	PMID[546035]
NPT146	Cell Line	SK-OV-3	Homo sapiens	GI50	n.a.	23768.4	nM	PMID[546035]
NPT396	Cell Line	T47D	Homo sapiens	GI50	n.a.	12882.5	nM	PMID[546035]
NPT397	Cell Line	NCI-H460	Homo sapiens	GI50	n.a.	16865.53	nM	PMID[546035]
NPT398	Cell Line	UACC-62	Homo sapiens	GI50	n.a.	13001.7	nM	PMID[546035]
NPT308	Cell Line	CAKI-1	Homo sapiens	GI50	n.a.	26607.25	nM	PMID[546035]
NPT399	Cell Line	SF-295	Homo sapiens	GI50	n.a.	12387.97	nM	PMID[546035]
NPT400	Cell Line	MDA-MB-435	Homo sapiens	GI50	n.a.	12912.19	nM	PMID[546035]
NPT458	Cell Line	IGROV-1	Homo sapiens	GI50	n.a.	16106.46	nM	PMID[546035]
NPT401	Cell Line	786-0	Homo sapiens	GI50	n.a.	17021.59	nM	PMID[546035]
NPT402	Cell Line	Hs-578T	Homo sapiens	GI50	n.a.	20558.91	nM	PMID[546035]
NPT403	Cell Line	UACC-257	Homo sapiens	GI50	n.a.	13152.25	nM	PMID[546035]
NPT404	Cell Line	CCRF-CEM	Homo sapiens	GI50	n.a.	16143.59	nM	PMID[546035]
NPT139	Cell Line	HT-29	Homo sapiens	GI50	n.a.	13740.42	nM	PMID[546035]
NPT405	Cell Line	NCI-H226	Homo sapiens	GI50	n.a.	11939.88	nM	PMID[546035]
NPT406	Cell Line	RXF 393	Homo sapiens	GI50	n.a.	17498.47	nM	PMID[546035]
NPT170	Cell Line	SK-MEL-28	Homo sapiens	GI50	n.a.	17338.04	nM	PMID[546035]
NPT407	Cell Line	COLO 205	Homo sapiens	GI50	n.a.	14354.89	nM	PMID[546035]
NPT439	Individual Protein	Butyrylcholinesterase	Homo sapiens	IC50	=	19460.0	nM	PMID[546036]
NPT66	Individual Protein	Acetylcholinesterase	Electrophorus electricus	Inhibition	=	24.52	%	PMID[546036]
NPT67	Individual Protein	Cholinesterase	Equus caballus	IC50	=	10780.0	nM	PMID[546036]
NPT67	Individual Protein	Cholinesterase	Equus caballus	Inhibition	=	66.21	%	PMID[546036]

☑ 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 NPC40488 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	148
0.1-0.2	917
0.2-0.3	2986
0.3-0.4	12364
0.4-0.5	20709
0.5-0.6	5086
0.6-0.7	463
0.7-0.8	22
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9449	High Similarity	NPC478140
0.7561	Intermediate Similarity	NPC56168
0.7541	Intermediate Similarity	NPC176012
0.75	Intermediate Similarity	NPC132847
0.75	Intermediate Similarity	NPC474164
0.7397	Intermediate Similarity	NPC311330
0.7305	Intermediate Similarity	NPC149379
0.7143	Intermediate Similarity	NPC150254
0.7143	Intermediate Similarity	NPC147000
0.7143	Intermediate Similarity	NPC226778
0.7143	Intermediate Similarity	NPC304761
0.7132	Intermediate Similarity	NPC292758
0.7132	Intermediate Similarity	NPC65855
0.7073	Intermediate Similarity	NPC324602
0.7068	Intermediate Similarity	NPC101139
0.7054	Intermediate Similarity	NPC95920
0.7054	Intermediate Similarity	NPC253645
0.7054	Intermediate Similarity	NPC147835
0.7054	Intermediate Similarity	NPC85001
0.7015	Intermediate Similarity	NPC472862
0.6992	Remote Similarity	NPC28280
0.6992	Remote Similarity	NPC304646
0.6984	Remote Similarity	NPC327226
0.698	Remote Similarity	NPC473922
0.6978	Remote Similarity	NPC307020
0.6977	Remote Similarity	NPC472980
0.6957	Remote Similarity	NPC109151
0.6944	Remote Similarity	NPC3202
0.6944	Remote Similarity	NPC313663
0.6942	Remote Similarity	NPC220596
0.6929	Remote Similarity	NPC472414
0.6923	Remote Similarity	NPC89769
0.6923	Remote Similarity	NPC259665
0.6923	Remote Similarity	NPC126859
0.6906	Remote Similarity	NPC472415
0.6901	Remote Similarity	NPC66177
0.6901	Remote Similarity	NPC8305
0.6901	Remote Similarity	NPC268763
0.6879	Remote Similarity	NPC119326
0.6879	Remote Similarity	NPC278097
0.6875	Remote Similarity	NPC42423
0.687	Remote Similarity	NPC24777
0.6855	Remote Similarity	NPC289140
0.6853	Remote Similarity	NPC124802
0.6846	Remote Similarity	NPC472979
0.6846	Remote Similarity	NPC159367
0.6846	Remote Similarity	NPC27252
0.6822	Remote Similarity	NPC243601
0.6821	Remote Similarity	NPC472103
0.6815	Remote Similarity	NPC93343
0.6797	Remote Similarity	NPC212799
0.6797	Remote Similarity	NPC19856
0.6794	Remote Similarity	NPC64642
0.6794	Remote Similarity	NPC472982
0.6794	Remote Similarity	NPC149455
0.6783	Remote Similarity	NPC71271
0.6783	Remote Similarity	NPC295478
0.6783	Remote Similarity	NPC116057
0.6781	Remote Similarity	NPC90693
0.6781	Remote Similarity	NPC64897
0.6776	Remote Similarity	NPC44649
0.6776	Remote Similarity	NPC328824
0.6776	Remote Similarity	NPC475578
0.6772	Remote Similarity	NPC474582
0.6772	Remote Similarity	NPC214200
0.6772	Remote Similarity	NPC228400
0.6746	Remote Similarity	NPC303611
0.6746	Remote Similarity	NPC91604
0.6746	Remote Similarity	NPC164514
0.6746	Remote Similarity	NPC290515
0.6746	Remote Similarity	NPC108606
0.6746	Remote Similarity	NPC226096
0.6733	Remote Similarity	NPC57976
0.6732	Remote Similarity	NPC264589
0.6731	Remote Similarity	NPC275839
0.6709	Remote Similarity	NPC217801
0.6692	Remote Similarity	NPC474695
0.6692	Remote Similarity	NPC471186
0.6692	Remote Similarity	NPC471133
0.6691	Remote Similarity	NPC9274
0.6691	Remote Similarity	NPC478138
0.669	Remote Similarity	NPC183722
0.6667	Remote Similarity	NPC472413
0.6642	Remote Similarity	NPC471189
0.6641	Remote Similarity	NPC469457
0.6641	Remote Similarity	NPC289117
0.6641	Remote Similarity	NPC46981
0.664	Remote Similarity	NPC329430
0.6615	Remote Similarity	NPC194390
0.6615	Remote Similarity	NPC224610
0.6615	Remote Similarity	NPC113326
0.6615	Remote Similarity	NPC212874
0.6615	Remote Similarity	NPC88267
0.6612	Remote Similarity	NPC60408
0.66	Remote Similarity	NPC153007
0.6596	Remote Similarity	NPC291027
0.6596	Remote Similarity	NPC213126
0.6596	Remote Similarity	NPC317474
0.6596	Remote Similarity	NPC169485
0.6596	Remote Similarity	NPC84281
0.6593	Remote Similarity	NPC478137
0.6585	Remote Similarity	NPC84171
0.6584	Remote Similarity	NPC73644
0.6581	Remote Similarity	NPC476757
0.6579	Remote Similarity	NPC471516
0.6577	Remote Similarity	NPC208725
0.6571	Remote Similarity	NPC326232
0.6569	Remote Similarity	NPC10286
0.6569	Remote Similarity	NPC213
0.6562	Remote Similarity	NPC135799
0.6561	Remote Similarity	NPC475763
0.6556	Remote Similarity	NPC211468
0.6556	Remote Similarity	NPC150712
0.6556	Remote Similarity	NPC170170
0.6556	Remote Similarity	NPC219233
0.6556	Remote Similarity	NPC239770
0.6554	Remote Similarity	NPC325568
0.6554	Remote Similarity	NPC228511
0.6544	Remote Similarity	NPC169616
0.6531	Remote Similarity	NPC246913
0.6525	Remote Similarity	NPC71684
0.6525	Remote Similarity	NPC314192
0.6524	Remote Similarity	NPC233650
0.6522	Remote Similarity	NPC235460
0.6522	Remote Similarity	NPC247858
0.6522	Remote Similarity	NPC474358
0.6522	Remote Similarity	NPC474387
0.6522	Remote Similarity	NPC257540
0.6522	Remote Similarity	NPC154511
0.6522	Remote Similarity	NPC137496
0.6519	Remote Similarity	NPC471188
0.6515	Remote Similarity	NPC142326
0.6515	Remote Similarity	NPC94751
0.6513	Remote Similarity	NPC323123
0.6512	Remote Similarity	NPC118275
0.651	Remote Similarity	NPC113325
0.651	Remote Similarity	NPC279045
0.6509	Remote Similarity	NPC329969
0.6508	Remote Similarity	NPC20142
0.6508	Remote Similarity	NPC58674
0.6508	Remote Similarity	NPC215351
0.6507	Remote Similarity	NPC69496
0.6503	Remote Similarity	NPC317654
0.6503	Remote Similarity	NPC96010
0.65	Remote Similarity	NPC477157
0.65	Remote Similarity	NPC477156
0.6497	Remote Similarity	NPC470274
0.6496	Remote Similarity	NPC246904
0.6489	Remote Similarity	NPC475239
0.6489	Remote Similarity	NPC315794
0.6485	Remote Similarity	NPC134858
0.6481	Remote Similarity	NPC79328
0.648	Remote Similarity	NPC314690
0.6479	Remote Similarity	NPC296686
0.6475	Remote Similarity	NPC477136
0.6475	Remote Similarity	NPC137096
0.6474	Remote Similarity	NPC2672
0.6474	Remote Similarity	NPC94602
0.6471	Remote Similarity	NPC470253
0.6467	Remote Similarity	NPC175870
0.6463	Remote Similarity	NPC126458
0.6457	Remote Similarity	NPC476903
0.6449	Remote Similarity	NPC473573
0.6447	Remote Similarity	NPC243162
0.6446	Remote Similarity	NPC195392
0.6439	Remote Similarity	NPC67043
0.6434	Remote Similarity	NPC35996
0.6429	Remote Similarity	NPC314992
0.6429	Remote Similarity	NPC164649
0.6429	Remote Similarity	NPC48342
0.642	Remote Similarity	NPC29647
0.6407	Remote Similarity	NPC150879
0.6407	Remote Similarity	NPC210140
0.6403	Remote Similarity	NPC469663
0.6403	Remote Similarity	NPC2265
0.6403	Remote Similarity	NPC92
0.64	Remote Similarity	NPC474811
0.64	Remote Similarity	NPC474787
0.64	Remote Similarity	NPC474855
0.64	Remote Similarity	NPC260045
0.64	Remote Similarity	NPC9687
0.64	Remote Similarity	NPC79465
0.64	Remote Similarity	NPC293377
0.64	Remote Similarity	NPC273907
0.64	Remote Similarity	NPC76785
0.64	Remote Similarity	NPC475598
0.64	Remote Similarity	NPC475318
0.64	Remote Similarity	NPC151706
0.64	Remote Similarity	NPC90194
0.64	Remote Similarity	NPC49577
0.64	Remote Similarity	NPC476102
0.64	Remote Similarity	NPC118099
0.6391	Remote Similarity	NPC475427
0.6389	Remote Similarity	NPC285394
0.6386	Remote Similarity	NPC2770
0.6386	Remote Similarity	NPC39103
0.6386	Remote Similarity	NPC169743
0.6385	Remote Similarity	NPC245927
0.6376	Remote Similarity	NPC233910
0.6376	Remote Similarity	NPC245836

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 NPC40488 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	109
0.1-0.2	504
0.2-0.3	785
0.3-0.4	2356
0.4-0.5	3350
0.5-0.6	1651
0.6-0.7	376
0.7-0.8	19
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8254	Intermediate Similarity	NPD2227	Clinical (unspecified phase)
0.8047	Intermediate Similarity	NPD1710	Approved
0.7752	Intermediate Similarity	NPD7522	Discontinued
0.771	Intermediate Similarity	NPD4416	Clinical (unspecified phase)
0.7597	Intermediate Similarity	NPD4031	Approved
0.7597	Intermediate Similarity	NPD4032	Approved
0.7586	Intermediate Similarity	NPD8131	Suspended
0.7576	Intermediate Similarity	NPD7725	Approved
0.7569	Intermediate Similarity	NPD3638	Discontinued
0.7424	Intermediate Similarity	NPD5511	Discontinued
0.7398	Intermediate Similarity	NPD4719	Phase 2
0.7328	Intermediate Similarity	NPD7508	Discontinued
0.7293	Intermediate Similarity	NPD2106	Clinical (unspecified phase)
0.7226	Intermediate Similarity	NPD6025	Phase 1
0.72	Intermediate Similarity	NPD3645	Discontinued
0.7143	Intermediate Similarity	NPD315	Approved
0.7143	Intermediate Similarity	NPD10	Approved
0.7143	Intermediate Similarity	NPD310	Approved
0.7143	Intermediate Similarity	NPD309	Approved
0.7143	Intermediate Similarity	NPD314	Approved
0.7143	Intermediate Similarity	NPD311	Approved
0.7143	Intermediate Similarity	NPD6775	Clinical (unspecified phase)
0.7111	Intermediate Similarity	NPD1922	Discontinued
0.7109	Intermediate Similarity	NPD4095	Clinical (unspecified phase)
0.7087	Intermediate Similarity	NPD5717	Approved
0.7075	Intermediate Similarity	NPD2174	Clinical (unspecified phase)
0.7059	Intermediate Similarity	NPD7342	Discontinued
0.7029	Intermediate Similarity	NPD2562	Approved
0.7029	Intermediate Similarity	NPD2561	Approved
0.7016	Intermediate Similarity	NPD4813	Approved
0.7016	Intermediate Similarity	NPD4263	Approved
0.6978	Remote Similarity	NPD4659	Approved
0.6972	Remote Similarity	NPD2606	Approved
0.6972	Remote Similarity	NPD2605	Approved
0.6967	Remote Similarity	NPD3718	Approved
0.6967	Remote Similarity	NPD3719	Approved
0.6966	Remote Similarity	NPD7431	Approved
0.6966	Remote Similarity	NPD7430	Approved
0.6957	Remote Similarity	NPD5351	Clinical (unspecified phase)
0.6957	Remote Similarity	NPD5618	Discontinued
0.6957	Remote Similarity	NPD5350	Clinical (unspecified phase)
0.6947	Remote Similarity	NPD4254	Approved
0.6947	Remote Similarity	NPD4025	Clinical (unspecified phase)
0.6947	Remote Similarity	NPD4253	Approved
0.6944	Remote Similarity	NPD7714	Approved
0.6944	Remote Similarity	NPD7715	Approved
0.6935	Remote Similarity	NPD713	Clinical (unspecified phase)
0.6923	Remote Similarity	NPD5156	Approved
0.6923	Remote Similarity	NPD5155	Approved
0.6901	Remote Similarity	NPD3637	Approved
0.6901	Remote Similarity	NPD3635	Approved
0.6901	Remote Similarity	NPD3636	Approved
0.6879	Remote Similarity	NPD3826	Clinical (unspecified phase)
0.6879	Remote Similarity	NPD4104	Clinical (unspecified phase)
0.6879	Remote Similarity	NPD4103	Phase 2
0.6871	Remote Similarity	NPD8154	Clinical (unspecified phase)
0.687	Remote Similarity	NPD551	Approved
0.687	Remote Similarity	NPD550	Approved
0.6853	Remote Similarity	NPD3594	Approved
0.6853	Remote Similarity	NPD3595	Approved
0.685	Remote Similarity	NPD854	Approved
0.685	Remote Similarity	NPD855	Approved
0.685	Remote Similarity	NPD5716	Approved
0.685	Remote Similarity	NPD4119	Approved
0.6846	Remote Similarity	NPD4725	Approved
0.6846	Remote Similarity	NPD6038	Clinical (unspecified phase)
0.6846	Remote Similarity	NPD4721	Approved
0.6846	Remote Similarity	NPD4726	Approved
0.6829	Remote Similarity	NPD3982	Approved
0.6829	Remote Similarity	NPD2878	Approved
0.6829	Remote Similarity	NPD3980	Approved
0.6828	Remote Similarity	NPD8118	Discontinued
0.6828	Remote Similarity	NPD6405	Approved
0.6828	Remote Similarity	NPD6407	Approved
0.6803	Remote Similarity	NPD3528	Clinical (unspecified phase)
0.68	Remote Similarity	NPD528	Clinical (unspecified phase)
0.6794	Remote Similarity	NPD4717	Approved
0.6794	Remote Similarity	NPD4720	Approved
0.6794	Remote Similarity	NPD4718	Approved
0.6786	Remote Similarity	NPD7249	Approved
0.6786	Remote Similarity	NPD7250	Approved
0.6781	Remote Similarity	NPD6623	Phase 3
0.6774	Remote Similarity	NPD4727	Phase 1
0.6769	Remote Similarity	NPD5705	Approved
0.6769	Remote Similarity	NPD5706	Approved
0.6769	Remote Similarity	NPD5704	Approved
0.6761	Remote Similarity	NPD1134	Approved
0.6761	Remote Similarity	NPD1133	Approved
0.6761	Remote Similarity	NPD1135	Approved
0.6761	Remote Similarity	NPD1131	Approved
0.6761	Remote Similarity	NPD1129	Approved
0.6757	Remote Similarity	NPD3552	Approved
0.6757	Remote Similarity	NPD3555	Approved
0.6757	Remote Similarity	NPD8147	Approved
0.6757	Remote Similarity	NPD3554	Approved
0.6757	Remote Similarity	NPD8148	Approved
0.6757	Remote Similarity	NPD3553	Approved
0.6746	Remote Similarity	NPD9612	Approved
0.6746	Remote Similarity	NPD9609	Approved
0.6746	Remote Similarity	NPD9611	Approved
0.6715	Remote Similarity	NPD317	Approved
0.6715	Remote Similarity	NPD856	Approved
0.6715	Remote Similarity	NPD318	Approved
0.6715	Remote Similarity	NPD16	Approved
0.6714	Remote Similarity	NPD3381	Discontinued
0.6711	Remote Similarity	NPD7488	Clinical (unspecified phase)
0.6711	Remote Similarity	NPD6676	Phase 2
0.671	Remote Similarity	NPD6222	Approved
0.671	Remote Similarity	NPD6221	Approved
0.6691	Remote Similarity	NPD5723	Approved
0.6689	Remote Similarity	NPD4257	Approved
0.6689	Remote Similarity	NPD8125	Discontinued
0.6689	Remote Similarity	NPD4256	Phase 2
0.6688	Remote Similarity	NPD8165	Discontinued
0.6667	Remote Similarity	NPD1371	Approved
0.6667	Remote Similarity	NPD4273	Approved
0.6667	Remote Similarity	NPD1374	Approved
0.6667	Remote Similarity	NPD1373	Approved
0.6667	Remote Similarity	NPD7997	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD4231	Approved
0.6667	Remote Similarity	NPD4229	Approved
0.6667	Remote Similarity	NPD7910	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD3683	Approved
0.6667	Remote Similarity	NPD6854	Phase 3
0.6667	Remote Similarity	NPD1370	Approved
0.6667	Remote Similarity	NPD4658	Approved
0.6667	Remote Similarity	NPD4479	Discontinued
0.6667	Remote Similarity	NPD4656	Approved
0.6667	Remote Similarity	NPD3681	Approved
0.6644	Remote Similarity	NPD6294	Approved
0.6644	Remote Similarity	NPD6295	Approved
0.6644	Remote Similarity	NPD5581	Approved
0.6643	Remote Similarity	NPD2956	Clinical (unspecified phase)
0.6642	Remote Similarity	NPD5162	Approved
0.6642	Remote Similarity	NPD4574	Approved
0.6642	Remote Similarity	NPD4576	Approved
0.664	Remote Similarity	NPD4814	Discontinued
0.6624	Remote Similarity	NPD7836	Clinical (unspecified phase)
0.6623	Remote Similarity	NPD3845	Phase 1
0.662	Remote Similarity	NPD4677	Discontinued
0.6619	Remote Similarity	NPD770	Discontinued
0.6614	Remote Similarity	NPD4117	Approved
0.6597	Remote Similarity	NPD2194	Approved
0.6597	Remote Similarity	NPD6259	Discontinued
0.6597	Remote Similarity	NPD2195	Approved
0.6596	Remote Similarity	NPD4216	Approved
0.6596	Remote Similarity	NPD2612	Approved
0.6596	Remote Similarity	NPD4215	Approved
0.6596	Remote Similarity	NPD2608	Approved
0.6596	Remote Similarity	NPD4217	Approved
0.6596	Remote Similarity	NPD3131	Approved
0.6596	Remote Similarity	NPD2610	Approved
0.6596	Remote Similarity	NPD2611	Approved
0.6596	Remote Similarity	NPD4218	Approved
0.6596	Remote Similarity	NPD3132	Approved
0.6596	Remote Similarity	NPD2609	Approved
0.6596	Remote Similarity	NPD2173	Clinical (unspecified phase)
0.6594	Remote Similarity	NPD828	Approved
0.6589	Remote Similarity	NPD4817	Approved
0.6589	Remote Similarity	NPD4818	Approved
0.6587	Remote Similarity	NPD2005	Discontinued
0.6587	Remote Similarity	NPD1738	Approved
0.6585	Remote Similarity	NPD5915	Approved
0.6577	Remote Similarity	NPD6544	Discontinued
0.6577	Remote Similarity	NPD823	Approved
0.6577	Remote Similarity	NPD6817	Clinical (unspecified phase)
0.6577	Remote Similarity	NPD817	Approved
0.6577	Remote Similarity	NPD2568	Approved
0.6571	Remote Similarity	NPD5238	Clinical (unspecified phase)
0.6562	Remote Similarity	NPD4227	Discontinued
0.6562	Remote Similarity	NPD1946	Clinical (unspecified phase)
0.6558	Remote Similarity	NPD7295	Approved
0.6554	Remote Similarity	NPD3110	Approved
0.6554	Remote Similarity	NPD3109	Approved
0.6547	Remote Similarity	NPD316	Approved
0.6532	Remote Similarity	NPD4543	Discontinued
0.6531	Remote Similarity	NPD3056	Clinical (unspecified phase)
0.6531	Remote Similarity	NPD8011	Discontinued
0.6525	Remote Similarity	NPD5576	Approved
0.6525	Remote Similarity	NPD5579	Approved
0.6522	Remote Similarity	NPD5500	Discontinued
0.6519	Remote Similarity	NPD4573	Approved
0.6519	Remote Similarity	NPD4571	Approved
0.6519	Remote Similarity	NPD4572	Approved
0.6516	Remote Similarity	NPD6609	Clinical (unspecified phase)
0.6516	Remote Similarity	NPD2422	Clinical (unspecified phase)
0.6515	Remote Similarity	NPD811	Approved
0.6515	Remote Similarity	NPD810	Approved
0.6515	Remote Similarity	NPD812	Approved
0.651	Remote Similarity	NPD6086	Phase 2
0.6507	Remote Similarity	NPD2613	Approved
0.65	Remote Similarity	NPD4093	Discontinued
0.65	Remote Similarity	NPD6026	Approved
0.6479	Remote Similarity	NPD3529	Phase 2
0.6479	Remote Similarity	NPD3974	Phase 2
0.6475	Remote Similarity	NPD4145	Approved
0.6475	Remote Similarity	NPD9613	Approved
0.6475	Remote Similarity	NPD4146	Approved
0.6475	Remote Similarity	NPD9616	Approved
0.6475	Remote Similarity	NPD6065	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